Indonesian occupation of East Timor



Indonesia occupied East Timor from December 1975 to October 1999. After centuries of Portuguese colonial rule in East Timor, a 1974 coup in Portugal led to decolonization among its former colonies, creating instability in East Timor and leaving its future uncertain. After a small-scale civil war, the pro-independence FRETILIN declared victory in the capital city of Dili and declared an independent East Timor on 28 November 1975.

Claiming its assistance had been requested by East Timorese leaders, Indonesian military forces invaded on 7 December and by 1979 had all but destroyed armed resistance to the occupation. Following a controversial "Popular Assembly" which many said was not a genuine act of self-determination, Indonesia declared the territory a province of Indonesia (Timor Timur).

For twenty-four years the Indonesian government subjected the people of East Timor to extrajudicial executions, routine and systematic torture, massacres and deliberate starvation. The 1991 Santa Cruz Massacre caused outrage around the world, and reports of other such killings were numerous. Resistance to Indonesian rule remained strong; in 1996 the Nobel Peace Prize was awarded to two men from East Timor, Carlos Filipe Ximenes Belo and José Ramos-Horta, for their ongoing efforts to peacefully end the occupation. A 1999 vote to determine East Timor's future resulted in an overwhelming majority in favor of independence, and in 2002 East Timor became an independent nation. The Commission for Reception, Truth and Reconciliation in East Timor estimated the number of deaths during the occupation from famine and violence to be between 90,800 and 202,600 including between 17,600 and 19,600 violent deaths or disappearances, out of a 1999 population of approximately 823,386. The truth commission held Indonesian forces responsible for about 70% of the violent killings.

Immediately after the invasion, the United Nations General Assembly and Security Council passed resolutions condemning Indonesia's actions and calling for immediate withdrawal. The governments of the United States, Australia, and United Kingdom were supportive of Indonesia throughout the occupation. Australia and Indonesia were the only nations in the world to recognise East Timor as a province of Indonesia, and soon afterwards began negotiations to divide resources found in the Timor Gap. Other governments, including Japan, Canada and Malaysia, also supported the Indonesian government. The invasion and suppression of East Timor's independence movement, however, caused great harm to Indonesia's reputation and international credibility.

After the 1999 vote for independence, paramilitary groups working with the Indonesian military undertook a final wave of violence during which most of the country's infrastructure was destroyed. The Australian led International Force for East Timor restored order and following the departure of Indonesian forces from East Timor, the United Nations Transitional Administration in East Timor administered the territory for two years, establishing a Serious Crimes Unit to investigate and prosecute crimes committed during 1999. Its limited scope and the small number of sentences delivered by Indonesian courts have caused numerous observers to call for an international tribunal for East Timor.

Background


The Portuguese first arrived in Timor in the 16th century, and in 1702 East Timor came under Portuguese colonial administration. Portuguese rule was tenuous until the island was divided with the Dutch Empire in 1860. A significant battleground during the Pacific War, East Timor was occupied by 20,000 Japanese troops. The fighting helped prevent a Japanese occupation of Australia, but resulted in 60,000 East Timorese deaths.

When Indonesia secured its independence after World War II under the leadership of Sukarno, it did not claim control of East Timor, and aside from general anti-colonial rhetoric it did not oppose Portuguese control of the territory. A 1959 revolt in East Timor against the Portuguese was not endorsed by the Indonesian government. A 1962 United Nations document notes: "the government of Indonesia has declared that it maintains friendly relations with Portugal and has no claim to Portuguese Timor...". These assurances continued after Suharto took power in 1965. An Indonesian official declared in December 1974: "Indonesia has no territorial ambition ... Thus there is no question of Indonesia wishing to annex Portuguese Timor."

In 1974, a coup in Lisbon caused significant changes in Portugal's relationship to its colony in Timor. The power shift in Europe invigorated movements for independence in colonies like Mozambique and Angola, and the new Portuguese government began a decolonization process for East Timor. The first of these was an opening of the political process.

FRETILIN, UDT, and APODETI
When East Timorese political parties were first legalised in April 1974, three groupings emerged as major players in the postcolonial landscape. The União Democrática Timorense (Timorese Democratic Union, or UDT), was formed in May by a group of wealthy landowners. Initially dedicated to preserving East Timor as a protectorate of Portugal, in September UDT announced its support for independence. A week later, the Frente Revolucionária de Timor-Leste Independente (Revolutionary Front for an Independent East Timor, or FRETILIN) appeared. Initially organised as the ASDT (Associacão Social Democrata Timorense), the group endorsed "the universal doctrines of socialism", as well as "the right to independence". As the political process grew more tense, however, the group changed its name and declared itself "the only legitimate representative of the people". The end of May saw the creation of a third party, Associacão Popular Democratica Timorense (Timorese Popular Democratic Association, or APODETI). Advocating East Timor's integration with Indonesia and originally named Associacão Integraciacao de Timor Indonesia (Association for the Integration of Timor into Indonesia), APODETI expressed concerns that an independent East Timor would then be economically weak and vulnerable.



Indonesian nationalist and military hardliners, particularly leaders of the intelligence agency Kopkamtib and special operations unit, Opsus, saw the Portuguese coup as an opportunity for East Timor's integration with Indonesia. The central government and military feared that an East Timor governed by leftists could be used as a base for incursions by unfriendly powers into Indonesia, and also that an independent East Timor within the archipelago could inspire secessionist sentiments within Indonesian provinces. The fear of national disintegration were played upon military leaders close to Suharto and remained as one of Indonesia's strongest justifications for refusing to entertain the prospect of East Timorese independence or even autonomy until the late 1990s. The military intelligence organisations initially sought a non-military annexation strategy, intending to use APODETI as its integration vehicle.

In January 1975, UDT and FRETILIN established a tentative coalition dedicated to achieving independence for East Timor. At the same time, the Australian government reported that the Indonesian military had conducted a "pre-invasion" exercise at Lampung. For months, the Indonesian Special Operations command, OPSUS, had been covertly supporting APODETI through Operasi Komodo (Operation Komodo, named after the lizard). By broadcasting accusations of communism among FRETILIN leaders and sowing discord in the UDT coalition, the Indonesian government fostered instability in East Timor and, observers said, created a pretext for invading. By May tensions between the two groups caused UDT to withdraw from the coalition.

In an attempt to negotiate a settlement to the dispute over East Timor's future, the Portuguese Decolonization Commission convened a conference in June 1975 in Macau. FRETILIN boycotted the meeting in protest of APODETI's presence; representatives of UDT and APODETI complained that this was an effort to obstruct the decolonization process. In his 1987 memoir Funu: The Unfinished Saga of East Timor, FRETILIN leader José Ramos-Horta recalls his "vehement protests" against his party's refusal to attend the meeting. "This", he writes, "was one of our tactical political errors for which I could never find an intelligent explanation."

Coup, civil war, and independence declaration
The tension reached a boiling point in mid-1975, when rumors began circulating of possible power seizures from both independence parties. In August 1975, UDT staged a coup in the capital city Dili and a small-scale civil war broke out. Ramos-Horta describes the fighting as "bloody", and details violence committed by both UDT and FRETILIN. He cites the International Committee of the Red Cross, which counted 2,000–3,000 people dead after the war. The fighting forced the Portuguese government onto the nearby island of Atauro. FRETILIN defeated UDT's forces after two weeks, much to the surprise of Portugal and Indonesia. UDT leaders fled to Indonesian-controlled West Timor. There they signed a petition on 7 September calling for East Timor's integration with Indonesia; most accounts indicate that UDT's support for this position was forced by Indonesia.



Once they had gained control of East Timor, FRETILIN faced attacks from the west, by Indonesian military forces—then known as Angkatan Bersenjata Republik Indonesia (ABRI)—and by a small group of UDT troops. Indonesia captured the border city of Batugadé on 8 October 1975; nearby Balibó and Maliana were taken eight days later. During the Balibó raid, members of an Australian television news crew—later dubbed the "Balibo Five"—were killed by Indonesian soldiers. Indonesian military officials say the deaths were accidental, and East Timorese witnesses say the journalists were deliberately killed. The deaths, and subsequent campaigns and investigations, attracted international attention and rallied support for East Timorese independence.

At the start of November, the foreign ministers from Indonesia and Portugal met in Rome to discuss a resolution of the conflict. Although no Timorese leaders were invited to the talks, FRETILIN sent a message expressing their desire to work with Portugal. The meeting ended with both parties agreeing that Portugal would meet with political leaders in East Timor, but the talks never took place. In mid-November, Indonesian forces began shelling the city of Atabae from the sea, and captured it by the end of the month.

Frustrated by Portugal's inaction, FRETILIN leaders believed they could ward off Indonesian advances more effectively if they declared an independent East Timor. National Political Commissioner Mari Alkatiri conducted a diplomatic tour of Africa, gathering support from governments there and elsewhere. According to FRETILIN, this effort yielded assurances from twenty-five countries—including the People's Republic of China, the Soviet Union, Mozambique, Sweden, and Cuba—to recognise the new nation. Cuba currently shares close relations with East Timor today. On 28 November 1975, FRETILIN unilaterally declared independence for the Democratic Republic of East Timor. Indonesia announced, UDT and APODETI leaders in and around Balibó would responded the next day by declaring that region independent from East Timor and officially part of Indonesia. But this Balibo Declaration was drafted by Indonesian intelligence and signed on Bali. Later this was described as the 'Balibohong Declaration', a pun on the Indonesian word for 'lie'. Portugal rejected both declarations, and the Indonesian government approved military action to begin its annexation of East Timor.

Invasion


On 7 December 1975, Indonesian forces invaded East Timor. Operasi Seroja (Operation Lotus) was the largest military operation ever carried out by that nation. Troops from FRETILIN's military organization FALINTIL engaged ABRI forces in the streets of Dili, and reported 400 Indonesian paratroopers were killed as they descended into the city. Angkasa Magazine reports 35 dead Indonesian troops, and 122 from the Fretilin side. By the end of the year, 10,000 troops occupied Dili and another 20,000 had been deployed throughout East Timor. Massively outnumbered, FALINTIL troops fled to the mountains and continued guerrilla combat operations. Indonesian soldiers in towns, particularly Dili, were reported to have indiscriminately killed civilians, including the rape and killing of women and children.



In March 1976, UDT leader Lopez da Cruz reported that 60,000 Timorese had been killed during the invasion. A delegation of Indonesian relief workers agreed with this statistic. In an interview on 5 April 1977 with the Sydney Morning Herald, Indonesian Foreign Minister Adam Malik said the number of dead was "50,000 people or perhaps 80,000".

The Indonesian government presented its annexation of East Timor as a matter of anticolonial unity. A 1977 booklet from the Indonesian Department of Foreign Affairs, entitled Decolonization in East Timor, paid tribute to the "sacred right of self-determination" and recognised APODETI as the true representatives of the East Timorese majority. It claimed that FRETILIN's popularity was the result of a "policy of threats, blackmail and terror". Later, Indonesian Foreign Minister Ali Alatas reiterated this position in his 2006 memoir The Pebble in the Shoe: The Diplomatic Struggle for East Timor. The island's original division into east and west, Indonesia argued after the invasion, was "the result of colonial oppression" enforced by the Portuguese and Dutch imperial powers. Thus, according to the Indonesian government, its annexation of the 27th province was merely another step in the unification of the archipelago which had begun in the 1940s.

UN response and international law
On the day following the invasion, a committee of the United Nations General Assembly convened to debate the situation. Nations allied with Indonesia—including India, Japan, and Malaysia—wrote a resolution blaming Portugal and the Timorese political parties for the bloodshed; it was rejected in favor of a draft prepared by Algeria, Cuba, Senegal, and Guyana, among others. This was adopted as GA Resolution 3485 (XXX) on 12 December, calling on Indonesia to "withdraw without delay". Ten days later the United Nations Security Council unanimously adopted Resolution 384 (1975), which echoes the GA resolution's call for an immediate Indonesian withdrawal. One year later the Security Council expressed the same sentiment in Resolution 389 (1976), and the General Assembly passed resolutions every year between 1976 and 1982 calling for self-determination in East Timor. Governments of large countries like China and the United States opposed further action; smaller countries like Costa Rica, Guinea-Bissau, and Iceland were the only delegations calling for strong enforcement of the resolutions. The 1982 resolution calls on the UN Secretary-General to "initiate consultations with all parties directly concerned, with a view to exploring avenues for achieving a comprehensive settlement of the problem".

Legal expert Roger S. Clark notes that Indonesia's invasion and occupation violated two key elements of international law: the right to self-determination and the prohibition on aggression. Neither the petition of 7 September 1975 calling for integration, nor the later resolution of the "People's Assembly" in May 1976, qualify as "informed and democratic processes impartially conducted and based on universal adult suffrage", as required by UN General Assembly Resolution 1541 (XV), which establishes the guidelines for the norms of self-determination. Other inadequacies existed in the petitions as well.

Indonesia's use of military force in East Timor is cited as a violation of Chapter I of the United Nations Charter, which states: "All Members shall refrain in their international relations from the threat or use of force against the territorial integrity or political independence of any state...." Some observers have argued that East Timor was not a state at the time of the invasion, and is thus not protected by the UN Charter. This claim mirrors those made against Indonesia by the Dutch during the Indonesian National Revolution. As legal scholar Susan Marks points out, if East Timor was considered a Portuguese colony, then although "there may be some doubt about the application of this provision [of UN Charter Chapter I] in the context of an armed conflict between a colonial power and its own colony, there can hardly be doubt that it applies to force by one sovereign state against another state's colony".

Indonesian hegemony
On 17 December, Indonesia formed the Provisional Government of East Timor (PGET) which was headed by Arnaldo dos Reis Araújo of APODETI as president and Lopez da Cruz of UDT. Most sources describe this institution as a creation of the Indonesian military. One of PGET's first activities was the formation of a "Popular Assembly" consisting of elected representatives and leaders "from various walks of Timorese life". Like the PGET itself, the Popular Assembly is usually characterised as an instrument of propaganda created by the Indonesian military; although international journalists were invited to witness the group's meeting in May 1976, their movement was tightly constrained. The Assembly drafted a request for formal integration into Indonesia, which Jakarta described as "the act of self-determination" in East Timor.

Indonesian campaigns against the resistance
Leaders of Indonesian intelligence influential with Suharto initially envisaged that invasion, subdual of Fretilin resistance, and integration with Indonesia would be quick and relatively painless. The ensuing Indonesian campaigns were devastating for the East Timorese, an enormous drain on Indonesian resources, severely damaging Indonesia internationally, and ultimately a failure. Schwarz suggests the fact that Indonesian military's power base remained barely dented by the mid-1970s intelligence miscalculations and ongoing failures, was a measure of the military's dominance of Indonesian affairs. East Timor was a training ground for the officer corps in tactics of suppression for Aceh and Papua, and was pivotal in ensuring military sector dominance of Indonesia.



Indonesia kept East Timor shut off from the rest of the world, except for a few years in the late 1980s and early 1990s, claiming that the vast majority of East Timorese supported integration. This position was followed closely by the Indonesian media such that an East Timorese acceptance of their integration with Indonesia was taken for granted by, and was a non-issue for, the majority of Indonesians.

Starting in September 1977, Indonesian forces began what Catholic officials in East Timor called an "encirclement and annihilation" campaign. 35,000 ABRI troops surrounded areas of FRETILIN support and killed hundreds of men, women, and children. Air and naval bombardments were followed by ground troops, who destroyed villages and agricultural infrastructure. Thousands of people may have been killed during this period. During a firefight with Indonesian troops in December 1978, FRETILIN's leader Nicolau Lobato was killed. His successor was Xanana Gusmão, who was instrumental in building the National Council of Maubere Resistance (CNRM), an umbrella structure for people and groups opposed to the occupation.

Indonesian forces moved hundreds of thousands of people into camps, where they were imprisoned and subjected to hunger. FRETILIN radio claimed Indonesian planes dropped chemical agents, and several observers—including the Bishop of Dili—reported seeing napalm dropped on the countryside. In 1981 the Indonesian military launched Operasi Keamanan (Operation Security), which some have named the "fence of legs" program. 50,000 East Timorese men and boys were ordered to march through the mountains, sweeping guerrillas into the central part of the region. The operation failed to crush the resistance, and popular resentment toward the occupation grew stronger than ever. As FRETILIN troops in the mountains continued their sporadic attacks, Indonesian forces carried out numerous operations to destroy them over the next ten years. In the cities and villages, meanwhile, a non-violent resistance movement began to take shape.

At the same time, Indonesian forces carried out a widespread campaign of killing, torture, forced disappearances, political imprisonment, and other abuses of human rights. Starting in 1981, Indonesian officials sent thousands of prisoners to Atauro Island, where Amnesty International described the conditions as "deplorable". Massacres by the Indonesian military have been documented across East Timor. In September 1981, 400 civilians were killed in Lacluta, and in August 1983, 200 people were burned alive in the village of Creras, with 500 others killed at a nearby river. An eyewitness who testified before the Australian Senate stated that soldiers deliberately killed small children by smashing their heads against a rock.

Those suspected of opposing integration were often arrested and tortured. In 1983 Amnesty International published an Indonesian manual it had received from East Timor instructing military personnel on how to inflict physical and mental anguish, and cautioning troops to "Avoid taking photographs showing torture (of someone being given electric shocks, stripped naked and so on)". In his 1997 memoir East Timor's Unfinished Struggle: Inside the Timorese Resistance, Constâncio Pinto describes being tortured by Indonesian soldiers: "With each question, I would get two or three punches in the face. When someone punches you so much and so hard, it feels as if your face is broken. People hit me on my back and on my sides with their hands and then kicked me.... [In another location] they psychologically tortured me; they didn't hit me, but they made strong threats to kill me. They even put a gun on the table." In Michele Turner's book Telling East Timor: Personal Testimonies 1942–1992, a woman named Fátima describes watching torture take place in a Dili prison: "They make people sit on a chair with the front of the chair on their own toes. It is mad, yes. The soldiers urinate in the food then mix it up for the person to eat. They use electric shock and they use an electric machine...."

Violence against women
Indonesian military abuses against women in East Timor were numerous and well-documented. In addition to suffering arbitrary detainment, torture, and extrajudicial execution, women faced rape and sexual abuse—sometimes for the crime of being related to an independence activist. The scope of the problem is difficult to ascertain, owing to the intense military control imposed during the occupation, compounded by the shame felt by victims. In a 1995 report on violence against women in Indonesia and East Timor, Amnesty International USA wrote: "Women are reluctant to pass on information to non-governmental organizations about rape and sexual abuse, let alone to report violations to the military or police authorities."

Other forms of violence against women took the form of harassment, intimidation, and enforced marriage. The Amnesty report cites the case of a woman forced to live with a commander in Baucau, then harassed daily by troops after her release. Such "marriages" took place regularly during the occupation. Women were also encouraged to accept sterilization procedures, and some were pressured to take the contraceptive Depo Provera, sometimes without full knowledge of its effects.

In 1999 researcher Rebecca Winters released the book Buibere: Voice of East Timorese Women, which chronicles many personal stories of violence and abuse dating to the earliest days of the occupation. One woman tells of being interrogated while stripped half-naked, tortured, molested, and threatened with death. Another describes being chained at the hands and feet, raped repeatedly, and interrogated for weeks. A woman who had prepared food for FRETILIN guerrillas was arrested, burned with cigarettes, tortured with electricity, and forced to walk naked past a row of soldiers into a tank filled with urine and feces.

Enforced starvation
With large sectors of the population forced into resettlement camps, food production was severely limited. Those in the camps were allowed to farm only a small area of land nearby, and constant re-use of soil made it barren. Hunger and starvation began to claim thousands of lives in the late 1970s. One church worker reported five hundred East Timorese dying of starvation every month in one district. World Vision Indonesia visited East Timor in October 1978 and claimed that 70,000 East Timorese were at risk of starvation. An envoy from the International Committee of the Red Cross reported in 1979 that 80 percent of one camp's population was malnourished, in a situation that was "as bad as Biafra". The ICRC warned that "tens of thousands" were at risk of starvation. Indonesia announced that it was working through the government-run Indonesian Red Cross to alleviate the crisis, but the NGO Action for World Development charged that organization with selling donated aid supplies.

In 2006 the UN's Commission for Reception, Truth and Reconciliation in East Timor released a 2,500-page report that accused the Indonesian military of using enforced starvation as a weapon to exterminate the East Timorese civilian population, and that large numbers of people were "positively denied access to food and its sources". The report, based on interviews with over 8,000 witnesses, as well as Indonesian military papers and intelligence from international sources, stated that the Indonesians used chemical weapons and napalm to poison food and water supplies. The group's final report cites testimony from individuals who were denied food, and details destruction of crops and livestock by Indonesian soldiers. It concluded that a minimum of 73,000 people died due to hunger and illness as a result of the occupation.

Abuses by FRETILIN
The Indonesian government reported in 1977 that several mass graves containing "scores" of people killed by FRETILIN had been found near Ailieu and Samé. Amnesty International confirmed these reports in 1985, and also expressed concern about several extrajudicial killings for which FRETILIN had claimed responsibility. In 1997 Human Rights Watch condemned a series of attacks carried out by FRETILIN, which led to the deaths of nine civilians.

Demography and economy


The Portuguese language was banned in East Timor and Indonesian was made the language of government, education and public commerce, and the Indonesian school curriculum was implemented. The official Indonesian national ideology, Pancasila, was applied to East Timor and government jobs were restricted to those holding certification in Pancasila training. East Timorese animist belief systems did not fit with Indonesia's constitutional monotheism, resulting in mass conversions to Christianity. Portuguese clergy were replaced with Indonesian priests and Latin and Portuguese mass was replaced by Indonesian mass. Before the invasion, less than 30 percent of East Timorese were Roman Catholics, and by the 1980s, 80 percent were registered as Catholics. With a 90 percent Catholic population, East Timor is currently one of the most densely Catholic countries in the world.

East Timor was a particular focus for the Indonesian government's transmigration program, which aimed to resettle Indonesians from densely to less populated regions. Media censorship under the "New Order" meant that the state of conflict in East Timor was unknown to the transmigrants, predominantly poor Javanese and Balinese wet-rice farmers. On arrival they found themselves under ongoing threat of attack by East Timorese resistance fighters, and became the object of local resentment, since large tracts of land belonging to East Timorese had been compulsorily appropriated by the Indonesian government for transmigrant settlement. Although many gave up and returned to their island of origin, those migrants that stayed in East Timor contributed to the "Indonesianisation" of East Timor's integration. 662 transmigrant families (2,208 people) settled in East Timor in 1993, whereas an estimated 150,000 free Indonesian settlers lived in East Timor by the mid-1990s, including those offered jobs in education and administration. Migration increased resentment amongst Timorese who were overtaken by more business savvy immigrants.

Following the invasion, Portuguese commercial interests were taken over by Indonesians. The border with West Timor was opened resulting in an influx of West Timorese farmers, and in January 1989 the territory was open to private investment. Economic life in the towns was subsequently brought under the control of entrepreneurial Bugis, Makassarese, and Butonese immigrants from South Sulawesi, while East Timor products were exported under partnerships between army officials Indonesian businessmen. Denok, a military-controlled firm, monopolised some of East Timor's most lucrative commercial activities, including sandal wood export, hotels, and the import of consumer products. The group's most profitable business, however, was its monopoly on the export of coffee, which was the territory's most valuable cash crop. Indonesian entrepreneurs came to dominate non-Denok/military enterprises, and local manufactures from the Portuguese period made way for Indonesian imports.

The Indonesian government's primary response to criticism of its policies was to highlight its funding of development in East Timor's health, education, communications, transportation, and agriculture. East Timor, however, remained poor following centuries of Portuguese colonial neglect and Indonesian critic George Aditjondro points out that conflict in the early years of occupation lead to sharp drops in rice and coffee production, and livestock populations. Other critics argue that infrastructure development, such as road construction, is often designed to facilitate Indonesian military and corporate interests. While the military controlled key businesses, private investors, both Indonesian and international, avoided the territory. Despite improvements since 1976, a 1993 Indonesian government report estimated that in three-quarters of East Timor's 61 districts, more than half lived in poverty.

Changing resistance and integration campaigns
Major investment by the Indonesian government to improve East Timor's infrastructure, and health and education facilities since 1975, did not end East Timorese resistance to Indonesian rule. Although by the 1980s Fretilin forces had dropped to a few hundred armed men, Fretilin increased its contacts with young Timorese especially in Dili, and an un-armed civil resistance seeking self-determination took shape. Many of those in the protest movements were young children at the time of the invasion and had been educated under the Indonesian system. They resented the repression of Timorese cultural and political life at the expense of the Indonesian, were ambivalent of Indonesian economic development, and spoke Portuguese amongst themselves, stressing their Portuguese heritage. Seeking help from Portugal for self-determination, they considered Indonesia an occupying force. Abroad, Fretilin's members—most notably former journalist José Ramos-Horta (later to be Prime Minister and President)—pushed their cause in diplomatic forums.

The reduced armed resistance prompted the Indonesian government in 1988 to open up East Timor to improve its commercial prospects, including a lifting of the travel ban on journalists. The new policy came from foreign minister Ali Alatas against the advice of the military leadership who feared it would lead to loss of control. Alatas and diplomats swayed Suharto of the policy as a response to international concerns. In late 1989, hardline military commander Brigadier General Mulyadi was replaced by Brigadier General Rudolph Warouw who promised a more "persuasive" approach to anti-integrationists. Restrictions on travel within the territory were reduced, groups of political prisoners were released, and the use of torture in interrogation became less common. Warouw attempted to increase military discipline; in February 1990 an Indonesian soldier was prosecuted for unlawful conduct in East Timor, the first such action since the invasion.

A reduced fear of persecution encouraged the resistance movements; anti-integration protests accompanied high-profile visits to East Timor including that of Pope John Paul II in 1989. The end of the Cold War removed much of the justification for western support of Indonesia's occupation. The resulting increase in international attention to self-determination and human rights put further pressure on Indonesia. Subsequent events within East Timor in the 1990s helped to dramatically raise the international profile of East Timor, which in turn significantly boosted the momentum of the resistance groups.

Santa Cruz massacre


During a memorial mass on 12 November 1991 for a pro-independence youth shot by Indonesian troops, demonstrators among the 2,500-strong crowd unfurled the Fretlin flag and banners with pro-independence slogans, and chanted boisterously but peacefully. Following a brief confrontation between Indonesian troops and protesters, 200 Indonesian soldiers opened fire on the crowd killing at least 250 Timorese.

The testimonies of foreigners at the cemetery were quickly reported to international news organisations, and video footage of the massacre was widely broadcast internationally causing outrage. In response to the massacre, activists around the world organised in solidarity with the East Timorese, and a new urgency was brought to calls for self-determination. TAPOL, a British organization formed in 1973 to advocate for democracy in Indonesia, increased its work around East Timor. In the United States, the East Timor Action Network (now the East Timor and Indonesia Action Network) was founded and soon had chapters in ten cities around the country. Other solidarity groups appeared in Portugal, Australia, Japan, Germany, Malaysia, Ireland, and Brazil. Coverage of the massacre was a vivid example of how growth of new media in Indonesia was making it increasingly difficult for the "New Order" to control information flow in and out of Indonesia, and that in the post-Cold War 1990s, the government was coming under increasing international scrutiny. A number of pro-democracy student groups and their magazines began to openly and critically discuss not just East Timor, but also the "New Order" and the broader history and future of Indonesia.

Sharp condemnation of the military came not just from the international community, but from within parts of the Indonesian elite. The massacre ended the governments 1989 opening of the territory and a new period of repression began. Warouw was removed from his position and his more accommodating approach to Timorese resistance rebuked by his superiors. Suspected Fretilin sympathisers were arrested, human rights abuses rose, and the ban on foreign journalists was reimposed. Hatred intensified amongst Timorese of the Indonesian military presence. Major General Prabowo's, Kopassus Group 3 trained militias gangs dressed in black hoods to crush the remaining resistance.

Arrest of Xanana Gusmão
On 20 November 1992 FRETILIN leader Xanana Gusmão was arrested by Indonesian troops. In May 1993 he was sentenced to life imprisonment for "rebellion", but his sentence was later commuted to 20 years. The arrest of the universally acknowledged leader of the resistance was a major frustration to the anti-integration movement in East Timor, but Gusmão continued to serve as a symbol of hope from inside the Cipinang prison. Nonviolent resistance by East Timorese, meanwhile, continued to show itself. When President Bill Clinton visited Jakarta in 1994, twenty-nine East Timorese students occupied the U.S. embassy to protest U.S. support for Indonesia.

At the same time, human rights observers called attention to continued violations by Indonesian troops and police. A 1995 report by Human Rights Watch noted that "abuses in the territory continue to mount", including torture, disappearances, and limitations on basic rights. After a series of riots in September and October 1995, Amnesty International criticised Indonesian authorities for a wave of arbitrary arrests and torture. The report indicates detainees were beaten with iron bars, kicked, lacerated, and threatened with death.



Nobel Peace Prize
In 1996 East Timor was suddenly brought to world attention when the Nobel Peace Prize was awarded to Bishop Carlos Filipe Ximenes Belo and José Ramos-Horta "for their work towards a just and peaceful solution to the conflict in East Timor". The Nobel Committee indicated in its press release that it hoped the award would "spur efforts to find a diplomatic solution to the conflict in East Timor based on the people's right to self-determination". As Nobel scholar Irwin Abrams notes:Diplomats from Indonesia and Portugal, meanwhile, continued the consultations required by the 1982 General Assembly resolution, in a series of meetings intended to resolve the problem of what Foreign Minister Ali Alatas called the "pebble in the Indonesian shoe".

End of Indonesian control
Renewed United Nations-brokered mediation efforts between Indonesia and Portugal began in early 1997.

Transition in Indonesia


Independence for East Timor, or even limited regional autonomy, was never going to be allowed under Suharto's New Order. Notwithstanding Indonesian public opinion in the 1990s occasionally showing begrudging appreciation of the Timorese position, it was widely feared that an independent East Timor would destabilise Indonesian unity. The 1997 Asian Financial Crisis, however, caused tremendous upheaval in Indonesia and led to Suharto's resignation in May 1998, ending his thirty-year presidency. Prabowo, by then in command of the powerful Indonesian Strategic Reserve, went into exile in Jordan and military operations in East Timor were costing the bankrupt Indonesian government a million dollars a day. The subsequent "reformasi" period of relative political openness and transition, included unprecedented debate about Indonesia's relationship with East Timor. For the remainder of 1998, discussion forums took place throughout Dili working towards a referendum. Foreign Minister Alatas, described plans for phased autonomy leading to possible independence as "all pain, no gain" for Indonesia. On 8 June 1998, three weeks after taking office, Suharto's successor B. J. Habibie announced that Indonesia would soon offer East Timor a special plan for autonomy.

In late 1998, the Australian Government of John Howard drafted a letter to Indonesia advising of a change in Australian policy, and advocating for the staging of referendum on independence within a decade. President Habibie saw such an arrangement as implying "colonial rule" by Indonesia and he decided to call a snap referendum on the issue.

Indonesia and Portugal announced on 5 May 1999 that it had agreed to hold a vote allowing the people of East Timor to choose between the autonomy plan or independence. The vote, to be administered by the United Nations Mission in East Timor (UNAMET), was originally scheduled for 8 August but later postponed until 30 August. Indonesia also took responsibility for security; this arrangement caused worry in East Timor, but many observers believe that Indonesia would have refused to allow foreign peacekeepers during the vote.

1999 referendum
As groups supporting autonomy and independence began campaigning, a series of pro-integration paramilitary groups of East Timorese began threatening violence—and indeed committing violence—around the country. Alleging pro-independence bias on the part of UNAMET, the groups were seen working with and receiving training from Indonesian soldiers. Before the May agreement was announced, an April paramilitary attack in Liquiça left dozens of East Timorese dead. On 16 May 1999, a gang accompanied by Indonesian troops attacked suspected independence activists in the village of Atara; in June another group attacked a UNAMET office in Maliana. Indonesian authorities claimed to be helpless to stop the violence between rival factions among the East Timorese, but Ramos-Horta joined many others in scoffing at such notions. In February 1999 he said: "Before [Indonesia] withdraws it wants to wreak major havoc and destabilization, as it has always promised. We have consistently heard that over the years from the Indonesian military in Timor."

As militia leaders warned of a "bloodbath", Indonesian "roving ambassador" Francisco Lopes da Cruz declared: "If people reject autonomy there is the possibility blood will flow in East Timor." One paramilitary announced that a vote for independence would result in a "sea of fire", an expression referring to the Bandung Sea of Fire during Indonesia's own war of independence from the Dutch. As the date of the vote drew near, reports of anti-independence violence continued to accumulate.

The day of the vote, 30 August 1999, was generally calm and orderly. 98.6 percent of registered voters cast ballots, and on 4 September UN Secretary-General Kofi Annan announced that 78.5 percent of the votes had been cast for independence. Brought up on the "New Order"'s insistence that the East Timorese supported integration, Indonesians were either shocked by, or disbelieved that the East Timorese had voted against being part of Indonesia. Many accepted media stories blaming the supervising United Nations and Australia who had pressured Habibie for a resolution.

Within hours of the results, paramilitary groups had begun attacking people and setting fires around the capital Dili. Foreign journalists and election observers fled, and tens of thousands of East Timorese took to the mountains. Islamic gangs attacked Dili's Catholic Diocese building, killing two dozen people; the next day, the headquarters of the ICRC was attacked and burned to the ground. Almost one hundred people were killed later in Suai, and reports of similar massacres poured in from around East Timor. The UN withdrew most of its personnel, but the Dili compound had been flooded with refugees. Four UN workers refused to evacuate unless the refugees were withdrawn as well, insisting they would rather die at the hands of the paramilitary groups. At the same time, Indonesian troops and paramilitary gangs forced over 200,000 people into West Timor, into camps described by Human Rights Watch as "deplorable conditions".

When a UN delegation arrived in Jakarta on 8 September, they were told by Indonesian President Habibie that reports of bloodshed in East Timor were "fantasies" and "lies". General Wiranto of the Indonesian military insisted that his soldiers had the situation under control, and later expressed his emotion for East Timor by singing the 1975 hit song "Feelings" at an event for military wives.

Indonesian withdrawal and peacekeeping force


The violence was met with widespread public anger in Australia, Portugal and elsewhere and activists in Portugal, Australia, the United States and other nations pressured their governments to take action. Australian Prime Minister John Howard consulted United Nations Secretary General Kofi Annan and lobbied U.S. President Bill Clinton to support an Australian led international peace keeper force to enter East Timor to end the violence. The United States offered crucial logistical and intelligence resources and an "over-horizon" deterrent presence, but did not commit forces to the operation. Finally, on 11 September, Bill Clinton announced:

I have made clear that my willingness to support future economic assistance from the international community will depend upon how Indonesia handles the situation from today.

Indonesia, in dire economic straits relented. President BJ Habibie announced on 12 September that Indonesia would withdraw Indonesian soldiers and allow an Australian-led international peacekeeping force to enter East Timor.

On 15 September 1999, the United Nations Security Council expressed concern at the deteriorating situation in East Timor, and issued UNSC Resolution 1264 calling for a multinational force to restore peace and security to East Timor, to protect and support the United Nations mission there, and to facilitate humanitarian assistance operations until such time as a United Nations peacekeeping force could be approved and deployed in the area.

The International Force for East Timor, or INTERFET, under the command of Australian Major General Peter Cosgrove, entered Dili on 20 September and by 31 October the last Indonesian troops had left East Timor. The arrival of thousands of international troops in East Timor caused the militia to flee across the border into Indonesia, from whence sporadic cross-border raids by the militia against INTERFET forces were conducted.

The United Nations Transitional Administration in East Timor (UNTAET) was established at the end of October and administered the region for two years. Control of the nation was turned over to the Government of East Timor and independence was declared on 20 May 2002. On 27 September of the same year, East Timor joined the United Nations as its 191st member state.

The bulk of the military forces of INTERFET were Australian—more than 5,500 troops at its peak, including an infantry brigade, with armoured and aviation support—while eventually 22 nations contributed to the force which at its height numbered over 11,000 troops. The United States provided crucial logistic and diplomatic support throughout the crisis, while the cruiser USS Mobile Bay protected the INTERFET naval fleet and a U.S. Marine infantry battalion of 1,000 men—plus organic armour and artillery—was also stationed off the coast aboard the USS Belleau Wood in order to provide a strategic reserve in the event of significant armed opposition.

International response
Indonesia used fear of communism to garner varying degrees of support among western countries, including the United States and Australia, for its East Timor invasion and occupation. The invasion and suppression of East Timor's independence movement caused great harm to Indonesia's reputation and international credibility. Criticism from the developing world undermined efforts in the 1980s to secure the Non-Aligned Movement chair which Suharto strongly desired for Indonesia and condemnation of Indonesia continued through the 1990s.

Australia
In September 1974, Australian Prime Minister Gough Whitlam met with Suharto and indicated that he would support Indonesia if it annexed East Timor. On 11 November 1975, the Whitlam government was dismissed. This placed restrictions on the caretaker government of Fraser. Until the results of the 13 December election were known any action required approval from both political parties and the Governor General. On 4 December 1975 Australia unsuccessfully sought a UN resolution to determine the independence of East Timor, the Australian Government evacuated Australians and other foreign nationals from Dili. José Ramos-Horta arrived in Darwin on 5 December saying that aid agencies the Australian Red Cross and Australian Society for Intercountry Aid Timor (ASIAT) had been banned from East Timor. In the same news conference Horta said that East Timor, Fretlin Government would not accept any UN assistance that included Australia.

After winning the December elections, the Fraser government took the approach that trade with Southeast Asia and political ties with Southeast Asia were too important to be put at risk for what was seen as a lost cause. Australia abstained from the 1976 and 1977 UN General Assembly Resolutions, and by 1978 became the only government to officially recognise East Timor as a province of Indonesia.



One year later, Australia and Indonesia began drafting a treaty to share resources in the Timor Gap. The treaty was signed in December 1989, with estimates ranging from one to seven billion barrels of oil to be secured. This agreement, along with general economic partnership with Indonesia, is frequently cited as a crucial factor for the Australian government's position. And yet given that nearly 60,000 East Timorese had died during the fighting between Australian and Japanese forces that followed the invasion of Timor by the Japanese during the Pacific War some Australians believed their government owed a special debt to the former Portuguese colony. James Dunn, a senior Foreign Affairs adviser to the Australian Parliament before and during the occupation, condemned the government's position, saying later: "What had been of vital strategic value in 1941 was, in 1974, irrelevant and dispensable." Some Australian World War II veterans protested the occupation for similar reasons.

Successive Australian governments saw good relations and stability in Indonesia (Australia's largest neighbour) as providing an important security buffer to Australia's north, but the East Timor issue complicated co-operation between the two nations. Australia provided important sanctuary to East Timorese independence advocates like Jose Ramos-Horta (who based himself in Australia during his exile). Australia's trade with Indonesia grew through the 1980s and the Keating Labor Government signed a security pact with Indonesia in 1995 and gave relations with Jakarta a high priority. The fall of Indonesian President Suharto and a shift in Australian policy by the Howard Government in 1998 helped precipitate a proposal for a referendum on the question of independence for East Timor. In late 1998, Prime Minister John Howard and Foreign Minister Alexander Downer drafted a letter to Indonesia setting out a change in Australian policy, suggesting that East Timor be given a chance to vote on independence within a decade. The letter upset Indonesian President B. J. Habibie, who saw it as implying Indonesia was a "colonial power" and he decided to announce a snap referendum. A UN sponsored referendum held in 1999 showed overwhelming approval for independence, but was followed by violent clashes and a security crisis, instigated by anti-independence militia. Australia then led a United Nations backed International Force for East Timor to end the violence and order was restored. While the intervention was ultimately successful, Australian-Indonesian relations would take several years to recover.

The Australian Labor Party altered its East Timor policy in 1999 and adopted a policy of support for East Timorese independence and opposition to the Indonesian presence there, through its Foreign Affairs spokesperson Laurie Brereton. Breretons' credibility was attacked by the governing Liberal-National Coalition government and its Foreign Affairs Minister Alexander Downer, and Prime Minister Howard. They were assisted in their campaign by the then-Labor-backbencher Kevin Rudd (who would later lead the Labor Party to victory in the 2007 Australian federal election).

Philippines
Owing its strong relation with Indonesia, the Philippines initially was cold in the issue. In fact, not only that it denied Jose Ramos-Horta entry in 1997 (when he was supposed to give a lecture to the University of the Philippines Diliman), the President back then even included him in the immigration blacklist.

However, with the wide spread support from various countries, the Philippines finally changed its policy. After the Timorese Independence, the Philippines contributed medical and logistics personnel to Interfet, rather than ground troops. The United Nations even named a Filipino, Lieutenant General Jaime Delos Santos, to command the full-fledged UN peacekeeping force which takes over from Interfet on Tuesday.

Sharing the same Roman Catholic heritage, the Philippines became a natural ally and has maintained good relationship until now. It has now lifted Jose Ramos-Horta from the blacklist, not to mention that he is frequently giving lectures in various universities in the Philippines, most notably in the University of the Philippines Diliman, Polytechnic University of the Philippines, De La Salle University and Ateneo de Davao University.

Portugal
The day after the invasion, Portugal cut diplomatic ties with Indonesia and went on to support UN resolutions condemning the invasion. However, in the late 1970s and early 1980s, the Portuguese government appeared reluctant to push the issue; American Indonesia specialist, Benedict Anderson suggests this stemmed from uncertainty at the time over its application to the European Community. Portugal's criticism mounted sharply from the mid-1980s, and due to public pressure, the country became one the highest profile campaigners in international forums for East Timorese self-determination. Throughout the 1990s, Portugal took part in UN-brokered mediations with Indonesia.

United States
In the mid-1970s, the United States was completing a retreat from Indochina. A staunchly anti-communist Indonesia was considered by the United States to be an essential counterweight, and friendly relations with the Indonesian government were considered more important than a decolonization process in East Timor. The United States also wanted to maintain its access to deep water straits running through Indonesia for undetectable submarine passage between the Indian and Pacific oceans.



On the day before the invasion, U.S. President Gerald R. Ford and U.S. Secretary of State Henry A. Kissinger met with Indonesian president Suharto and reportedly gave their approval for the invasion. In response to Suharto saying "We want your understanding if it was deemed necessary to take rapid or drastic action [in East Timor]." Ford replied, "We will understand and not press you on the issue. We understand the problem and the intentions you have." Kissinger similarly agreed, though he had fears that the use of US-made arms in the invasion would be exposed to public scrutiny, talking of their desire to "influence the reaction in America" so that "there would be less chance of people talking in an unauthorised way." The US also hoped the invasion would be swift and not involve protracted resistance. "It is important that whatever you do succeeds quickly," Kissinger said to Suharto. Kissinger's main fear appears to have been that a violent take-over by the partly communist FRETILIN party might inspire similar Communist victories throughout Asia and possibly even lead to secessionist revolts threatening the very survival of Indonesia as a state.

The US supplied weapons to Indonesia during the invasion and the subsequent occupation. A week after the invasion of East Timor, the National Security Council prepared a detailed analysis which found that the vast majority of the military equipment was U.S. supplied. While the US government said they had suspended military assistance from December 1975 to June 1976, military aid was actually above what the US Department of State proposed and the US Congress continued to increase it, nearly doubling it. Between 1975 and 1980, when the violence in East Timor was at its climax, the United States furnished approximately $340 million in weaponry to the Indonesian government. US military aid and arms sales to Indonesia increased from 1974 and continued through to the Bush and Clinton years until it was stopped in 1999. US arms provisions to Indonesia between 1975 and 1995 amounted to approximately $1.1 billion.

The UN's Commission for Reception, Truth and Reconciliation in East Timor (CAVR) stated in the "Responsibility" chapter of its final report that U.S. "political and military support were fundamental to the Indonesian invasion and occupation" of East Timor between 1975 and 1999. The report (p. 92) also stated that "U.S. supplied weaponry was crucial to Indonesia's capacity to intensify military operations from 1977 in its massive campaigns to destroy the Resistance in which aircraft supplied by the United States played a crucial role."

Fretilin has claimed that the degree of U.S. support for the Indonesian government's efforts in East Timor may have extended beyond that of diplomatic support and material assistance. A UPI report from Sydney, Australia dated 19 June 1978, quoted a Fretilin press release, which stated: "American military advisers and mercenaries fought alongside Indonesian soldiers against FRETILIN in two battles ... In the meantime, American pilots are flying OV-10 Bronco aircraft for the Indonesian Air Force in bombing raids against the liberated areas under FRETILIN control."

The United States abstained from most of the UN resolutions censuring the Indonesian invasion. Daniel Patrick Moynihan, the U.S. Ambassador to the UN at the time, wrote later in his memoirs: "The Department of State desired that the United Nations prove utterly ineffective in whatever measures it undertook. This task was given to me, and I carried it forward with no inconsiderable success."



Other countries
Britain, Canada, Japan, and other nations supported Indonesia during the occupation of East Timor. Britain abstained from all of the UN General Assembly resolutions relating to East Timor, and sold arms throughout the occupation. In 1978 Indonesia purchased eight BAE Hawk jet trainers, which were used during the "encirclement and annihilation" campaign. Britain sold dozens of additional jets to Indonesia in the 1990s. Canada abstained from early General Assembly resolutions about East Timor, and opposed three. The Canadian government regularly sold weapons to Indonesia during the occupation, and in the 1990s approved over CDN$400 million in exports for spare weapons parts. Japan voted against all eight General Assembly resolutions regarding East Timor.

The Indian government also supported Indonesia, likening the occupation to its own seizure of Goa in 1961. Some analysts remarked that Indonesia's delayed action also prevented peaceful transfer of East Timor to it, similar to the manner in which the French transferred Pondicherry to India in 1962.

Member nations of the Association of Southeast Asian Nations (ASEAN), consistently voted against the General Assembly resolutions calling for self-determination in East Timor.

Number of deaths
Precise estimates of the death toll are difficult to determine. The 2005 report of the UN's Commission for Reception, Truth and Reconciliation in East Timor (CAVR) reports a figure of at least 90,800: 17,600 unlawful executions and 73,200 starvation deaths (applying the study's margin of error). CAVR did not estimate an upper limit though it speculated that this could have been as high as 202,600. The truth commission held Indonesian forces responsible for about 70% of the violent killings.

Researcher Ben Kiernan says that "a toll of 150,000 is likely close to the truth," although one can throw out an estimate of 200,000 or higher. The Center for Defense Information also estimated a total close to 150,000. A 1974 Catholic church estimate of the population of East Timor was 688,711 people; in 1982 the church reported only 425,000. This led to an estimate of 200,000 people killed during the occupation, which was widely reported around the world. Other sources such as Amnesty International and Human Rights Watch also support an estimate of over 200,000 killed.

According to specialist Gabriel Defert on the basis of statistical data available from the Portuguese and Indonesian authorities, and from the Catholic Church, between December 1975 and December 1981, approximately 308,000 Timorese lost their lives; this constituted about 44% of the pre-invasion population. Similarly Indonesian Professor George Aditjondro, formerly of Salatiga University in Java, concluded from his study of Indonesian Army data that in fact 300,000 Timorese had been killed in the early years of the occupation.

Robert Cribb of the Australian National University argues that the toll was significantly exaggerated. He argues that the 1980 census that counted 555,350 Timorese, although "the most reliable source of all," was probably a minimum rather than a maximum estimate for the total population. "It is worth recalling that hundreds of thousands of East Timorese disappeared during the violence of September 1999, only to reappear later," he writes. The 1980 census becomes more improbable in the face of the 1987 census that counted 657,411 Timorese – this would require a growth rate of 2.5% per year, nearly identical to the very high growth rate in East Timor from 1970 to 1975, and a highly unlikely one given the conditions of the brutal occupation, including Indonesian efforts to discourage reproduction. Noting the relative lack of personal accounts of atrocities or of traumatized Indonesian soldiers, he further adds that East Timor "does not appear—on the basis of news reports and academic accounts—to be a society traumatized by mass death...the circumstance leading up to the Dili massacre of 1991...indicate a society which retained its vigor and indignation in a way which would probably not have been possible if it had been treated as Cambodia was treated under Pol Pot." Even Indonesian military strategy was based on winning the "hearts and minds" of the population, a fact that does not support charges of mass killing.

Kiernan, starting from a base population of 700,000 Timorese in 1975 (based on the 1974 Catholic Church census) calculated an expected 1980 population of 735,000 Timorese (assuming a growth rate of only 1% per year as a result of the occupation). Accepting the 1980 count that Cribb regards as at least 10% (55,000) too low, Kiernan concluded that as many as 180,000 may have died in the war. Cribb argued that the 3% growth rate suggested by the 1974 census was too high, citing the fact that the church had previously postulated a growth rate of 1.8%, which would have produced a figure in line with the Portuguese population estimate of 635,000 for 1974.

Although Cribb maintained that the Portuguese census was almost certainly an underestimate, he believed it to be more likely correct than the church census, due to the fact that any church attempt to extrapolate the size of the total population "must be seen in light of its incomplete access to society" (less than half of Timorese were Catholic). Assuming a growth rate in line with the other nations of South East Asia, then, would yield a more accurate figure of 680,000 for 1975, and an expected 1980 population of slightly over 775,000 (without accounting for the decline in the birth rate resulting from the Indonesian occupation). The deficit remaining would be almost exactly 200,000. According to Cribb, Indonesian policies restricted the birth rate by up to 50% or more, thus around 45,000 of these were not born rather than killed; another 55,000 were "missing" as a result of the Timorese evading the Indonesian authorities who conducted the 1980 census. A variety of factors—the exodus of tens of thousands from their homes to escape FRETELIN in 1974-5; the deaths of thousands in the civil war; the deaths of combatants during the occupation; killings by FRETELIN; and natural disasters—diminish further still the civilian toll attributable to Indonesian forces during this time. Considering all this data, Cribb argues for a much lower toll of 100,000 or less, with an absolute minimum of 60,000, and a mere tenth of the civilian population dying unnaturally, for the years 1975–80.

Kiernan responded, however, by asserting that the influx of migrant workers during the occupation and the increase in the population growth rate typical of a mortality crisis justifies accepting the 1980 census as valid despite the 1987 estimate, and that the 1974 church census—though a "possible maximum"—cannot be discounted because the church's lack of access to society might well have resulted in an undercount. He concluded that at least 116,000 combatants and civilians were killed by all sides or died "unnatural" deaths from 1975–80 (if true, this would yield the result that about 15% of the civilian population of East Timor was killed from 1975–80). F. Hiorth separately estimated that 13% (95,000 out of an expected 730,000 when accounting for the reduction in birth rates) of the civilian population died during this period. Kiernan believes that the deficit was most probably around 145,000 when accounting for the reduction in birth rates, or 20% of East Timor's population. The mid-value of the UN report is 146,000 deaths; R.J. Rummel, an analyst of political killings, estimates 150,000.

Many observers have called the Indonesian military action in East Timor an example of genocide. In a study of the word's legal meaning and applicability to the occupation of East Timor, legal scholar Ben Saul concludes that because no group recognised under international law was targeted by the Indonesian authorities, a charge of genocide cannot be applied. However, he also notes: "The conflict in East Timor most accurately qualifies as genocide against a ‘political group’, or alternatively as ‘cultural genocide’, yet neither of these concepts are explicitly recognised in international law." The occupation has been compared to the killings of the Khmer Rouge, the Yugoslav wars, and the Rwandan Genocide.

Accurate numbers of Indonesian casualties are not known, however, some estimate up to 10,000 Indonesian troops died during the 1976–80 period. Rummel estimates that 10–15,000 Indonesians died in the war. The complete names of around 2,300 Indonesian soldiers and pro-Indonesian militias killed during the entire occupation is engraved into the Seroja Monument located in Armed Forces Headquarters in Cilangkap, south of Jakarta.

Justice
Saul goes on to discuss prosecutions of responsible parties for "crimes against humanity, war crimes, and other gross violations of human rights". In the years after the end of the occupation, a number of proceedings have been carried out to such an end. The 1999 UN Security Council resolution authorizing UNTAET described the history of "systematic, widespread and flagrant violations of international and human rights law" and demanded "that those responsible for such violence be brought to justice". To achieve these ends, UNTAET established a Serious Crimes Unit (SCU), which has attempted to investigate and prosecute individuals responsible for such violence. However, the SCU has been criticised for accomplishing relatively little, presumably because it is funded inadequately, limited in mandate to crimes committed only in 1999, and for other reasons. Indonesian trials purporting to punish those responsible for the violence were described as "manifestly inadequate" by a UN commission.

Deficiencies in these processes have led a number of organizations to call for an international tribunal to prosecute individuals responsible for killings in East Timor, similar to those established in Yugoslavia and Rwanda. A 2001 editorial by the East Timor NGO La'o Hamutuk said: An uncountable number of Crimes Against Humanity were committed during the 1975–1999 period in East Timor. Although an international court could not pursue all of them, it ... [would] confirm that the invasion, occupation and destruction of East Timor by Indonesia was a long-standing, systematic, criminal conspiracy, planned and ordered at the highest levels of government. Many of the perpetrators continue to wield authority and influence in East Timor’s nearest neighbor. The future of peace, justice and democracy in both East Timor and Indonesia depends on holding the highest-level perpetrators accountable.

In 2005, the Indonesia-Timor Leste Commission of Truth and Friendship was set up with the goal of establishing the truth relating to crimes under the occupation, and healing divisions between the countries. It has received criticism from NGOs and was rejected by the United Nations for offering impunity.

Indonesian governors of East Timor

 * President of the Provisional Government:
 * 17 December 1975 – 17 July 1976: Arnaldo dos Reis Araújo
 * Governors:
 * 1976 – 1978: Arnaldo dos Reis Araújo
 * 1978 – 1982: Guilherme Maria Gonçalves
 * 18 September 1982 – 18 September 1992: Mário Viegas Carrascalão
 * 18 September 1992 – 25 October 1999: José Abílio Osório Soares