Black site



In military terminology, a black site is a location at which an unacknowledged black project is conducted. Recently, the term has gained notoriety in describing secret prisons operated by the United States Central Intelligence Agency (CIA), generally outside of U.S. territory and legal jurisdiction. It can refer to the facilities that are controlled by the CIA used by the U.S. government in its "War on Terror" to detain alleged unlawful enemy combatants.

U.S. President George W. Bush acknowledged the existence of secret prisons operated by the CIA during a speech on September 6, 2006. A claim that the black sites existed was made by The Washington Post in November 2005 and before this by human rights NGOs (non-governmental organizations).

Many European countries have officially denied they are hosting black sites to imprison suspects or cooperating in the U.S. extraordinary rendition program. Not one country has confirmed that it is hosting black sites. However, a European Union (EU) report adopted on February 14, 2007, by a majority of the European Parliament (382 MEPs voting in favour, 256 against and 74 abstaining) stated the CIA operated 1,245 flights and that it was not possible to contradict evidence or suggestions that secret detention centres were operated in Poland and Romania.

In January 2012, Poland's Prosecutor General's office initiated investigative proceedings against Zbigniew Siemiątkowski, the former Polish intelligence chief. Siemiątkowski is charged with facilitating the alleged CIA detention operation in Poland, where foreign suspects may have been tortured in the context of the War on Terror. The possible involvement of Leszek Miller, Poland's Prime Minister in 2001-2004, is also considered.

Official recognition of black sites
Black sites operated by the U.S. government and its surrogates were first officially acknowledged by U.S. President George W. Bush in the fall of 2006. The International Committee of the Red Cross reported details of black site practices to the U.S. government in early 2007, and the contents of that report became public in March, 2009.

2006 Bush announcement
On September 6, 2006, Bush publicly admitted the existence of secret prisons and announced that many of the detainees held there were being transferred to Guantanamo Bay''.

2007 Red Cross report to the U.S. government
The International Committee of the Red Cross (ICRC) prepared a report based on interviews with black site detainees, conducted between October 6 and 11 and December 4 and 14, 2006, after their transfer to Guantanamo Bay. The report was submitted to Bush administration officials.

On March 15, 2009, Mark Danner provided a report in the New York Review of Books (with an abridged version in the New York Times) describing and commenting on the contents of the ICRC report. According to Danner, the report was marked "confidential" and was not previously made public before being made available to him. Danner provided excerpts of interviews with detainees, including Abu Zubaydah, Walid bin Attash and Khalid Shaikh Mohammed. Danner also provided excerpts of the ICRC report characterizing procedures used at the black sites, dubbed "an alternative set of procedures" by President George Bush, and discussed whether they fit the definition of torture.

Controversy over the legality and secrecy of black sites
Black sites are embroiled in controversy over the legal status of the detainees held there, the legal authority for the operation of the sites (including the collaboration between governments involved), and full (or even minimal) disclosure by the governments involved.

Legal status of black site detainees
An important aspect of black site operation is that the legal status of black site detainees is not clearly defined.

The revelation of such black sites adds to the controversy surrounding US government policy regarding those whom it describes as "unlawful enemy combatants". According to government sources, the detainees are broken into two groups. Approximately 30 detainees are considered the most dangerous or important terrorism suspects and are held by the CIA at black sites under the most secretive arrangements. The second group is more than 70 detainees who may have originally been sent to black sites, but were soon delivered by the CIA to intelligence agencies in allied Middle Eastern and Asian countries such as Afghanistan, Morocco, and Egypt. A further 100 ghost detainees kidnapped in Europe and "rendered" to other countries must be counted, according to Swiss senator Dick Marty's report of January 2006. This process is called "extraordinary rendition". Marty also underlined that European countries probably had knowledge of these covert operations. Furthermore, the CIA apparently financially assists and directs the jails in these countries. While the US and host countries have signed the United Nations Convention Against Torture, CIA officers are allowed to use what the agency calls "enhanced interrogation techniques". These have been alleged to constitute "severe pain or suffering" under the UN convention, which would be a violation of the treaty and thus US law.

Legal authority for black site operation
There is little or no stated legal authority for the operation of black sites by the United States or the other countries believed to be involved. In fact, the specifics of the network of black sites remains controversial. The United Nations has begun to intervene in this aspect of black sites.

The fourteen European countries Marty listed as collaborators in "unlawful inter-state transfers" are Great Britain, Germany, Isle of Man, Italy, Sweden, Bosnia, Republic of Macedonia, Turkey, Spain, Cyprus, Ireland, Greece, Portugal, Romania and Poland. Named airport bases include Glasgow Prestwick Airport (Britain), Shannon (Ireland), Ramstein and Frankfurt (Germany), Aviano Air Base (Italy), Palma de Mallorca Airport (Spain), Tuzla Air Base (Bosnia-Herzegovina), Skopje (Republic of Macedonia), Athens (Greece), Larnaca (Cyprus), Prague (Czech Republic), Stockholm, as well as Rabat (Morocco) and Algiers (Algeria). Polish Prime Minister Kazimierz Marcinkiewicz characterized the accusation as "libel", while Romania similarly said there was no evidence.

British Prime Minister Tony Blair said that the report "added absolutely nothing new whatever to the information we have". Poland and Romania received the most direct accusals, as the report claims the evidence for these sites is "strong". The report cites airports in Timişoara, Romania, and Szymany, Poland, as "detainee transfer/drop-off point[s]". Eight airports outside Europe are also cited.

On May 19, 2006, the United Nations Committee Against Torture (the U.N. body that monitors compliance with the UN Convention Against Torture) recommended that the United States cease holding detainees in secret prisons and stop the practice of rendering prisoners to countries where they are likely to be tortured. The decision was made in Geneva following two days of hearings at which a 26-member U.S. delegation defended the practices.

Public information about black site operation
The U.S. government does not provide information about the operation of black sites, and for a period of time did not provide information about the existence of black sites.

Representations by the Bush administration
Responding to the allegations about black sites, Secretary of State Condoleezza Rice stated on December 5, 2005, that US had not violated any country's sovereignty in the rendition of suspects, and that individuals were never rendered to countries where it was believed that they might be tortured. Some media sources have noted her comments do not exclude the possibility of covert prison sites operated with the knowledge of the "host" nation, or the possibility that promises by such "host" nations that they will refrain from torture may not be genuine. On September 6, 2006, Bush publicly admitted the existence of the secret prisons and that many of the detainees held there were being transferred to Guantanamo Bay.

In December 2002, The Washington Post reported that "the capture of al Qaeda leaders Ramzi bin al-Shibh in Pakistan, Omar al-Faruq in Indonesia, Abd al-Rahim al-Nashiri in Kuwait and Muhammad al Darbi in Yemen were all partly the result of information gained during interrogations." The Post cited "U.S. intelligence and national security officials" in reporting this.

On April 21, 2006, Mary O. McCarthy, a longtime CIA analyst, was fired for allegedly leaking classified information to a Washington Post reporter, Dana Priest, who was awarded the Pulitzer Prize for her revelations concerning the CIA's black sites. Some have speculated that the information allegedly leaked may have included information about the camps. McCarthy's lawyer, however, claimed that McCarthy "did not have access to the information she is accused of leaking". The Washington Post posited that McCarthy "had been probing allegations of criminal mistreatment by the CIA and its contractors in Iraq and Afghanistan", and became convinced that "CIA people had lied" in a meeting with US Senate staff in June 2005.

In a September 29, 2006, speech, Bush stated: "Once captured, Abu Zubaydah, Ramzi bin al-Shibh, and Khalid Sheikh Mohammed were taken into custody of the Central Intelligence Agency. The questioning of these and other suspected terrorists provided information that helped us protect the American people. They helped us break up a cell of Southeast Asian terrorist operatives that had been groomed for attacks inside the United States. They helped us disrupt an al Qaeda operation to develop anthrax for terrorist attacks. They helped us stop a planned strike on a U.S. Marine camp in Djibouti, and to prevent a planned attack on the U.S. Consulate in Karachi, and to foil a plot to hijack passenger planes and to fly them into Heathrow Airport and London's Canary Wharf."

On July 20, 2007, Bush made an executive order banning torture of captives by intelligence officials.

In a September 7, 2007, public address to the Council on Foreign Relations in New York, rare for a sitting Director of Central Intelligence, General Michael Hayden praised the program of detaining and interrogating prisoners, and credited it with providing 70 percent of the National Intelligence Estimate on the threat to America released in July. Hayden said the CIA has detained fewer than 100 people at secret facilities abroad since 2002, and even fewer prisoners have been secretly transferred to or from foreign governments. In a 20-minute question-and-answer session with the audience, Hayden disputed assertions that the CIA has used waterboarding, stress positions, hypothermia and dogs to interrogate suspects&mdash;all techniques that have been broadly criticized. "That's a pretty good example of taking something to the darkest corner of the room and not reflective of what my agency does" Hayden told one person from a human rights organization.

Information derived from investigative reporting
The vast majority of information that has been provided to the public about black sites has been the result of investigative reporting. For full details, see the section below on the media and investigative history.

Specific facts surrounding black sites
As discussed in the preceding section, many of the facts surrounding black sites remain controversial. The identity of detainees and the location of sites are known with varying degrees of certainty, though many facts have been discovered in substantial detail.

Detainees
The list of those thought to be held by the CIA include suspected al-Qaeda members Khalid Shaikh Mohammed, Nurjaman Riduan Isamuddin, Ramzi bin al-Shibh and Abu Zubaydah. The total number of ghost detainees is presumed to be at least one hundred, although the precise number cannot be determined because fewer than 10% have been charged or convicted. However, Swiss senator Dick Marty's memorandum on "alleged detention in Council of Europe states" stated that about 100 persons have been kidnapped by the CIA on European territory and subsequently rendered to countries where they may have been tortured. This number of 100 persons does not overlap, but adds itself to the U.S.-detained 100 ghost detainees.

A number of the alleged detainees listed above were transferred to the U.S.-run Guantanamo Bay prison on Cuba in the fall of 2006. With this publicly announced act, the United States government de facto also acknowledged the existence of secret prisons abroad in which these prisoners were held.

Khaled el-Masri
Khalid El-Masri is a German citizen who was detained, flown to Afghanistan, interrogated and allegedly tortured by the CIA for several months, and then released in remote Albania in May 2004 without having been charged with any offense. This was apparently due to a misunderstanding that arose concerning the similarity of the spelling of El-Masri's name with the spelling of suspected terrorist Khalid al-Masri. Germany had issued warrants for 13 people suspected to be involved with the abduction, but dropped them in September 2007.

On October 9, 2007, the U.S. Supreme Court declined without comment to hear an appeal of El-Masri's civil lawsuit against the United States (El-Masri v. Tenet), letting stand an earlier verdict by a federal district court judge, which was upheld by the U.S. Court of Appeals for the Fourth Circuit. Those courts had agreed with the government that the case could not go forward without exposing state secrets. In May 2007, Masri was committed to a psychiatric institution after he was arrested in the southern German city of Neu-Ulm on suspicion of arson. His attorney blamed his troubles on the CIA, saying the kidnapping and detention had left Masri a "psychological wreck".

See also: Murat Kurnaz

Imam Rapito
The CIA abducted Hassan Mustafa Osama Nasr (also known as Abu Omar) in Milan and transferred him to Egypt, where he was allegedly tortured and abused. Hassan Nasr was released by an Egyptian court&mdash;who considered his detention "unfounded"&mdash;in February 2007 and has not been indicted for any crime in Italy. Ultimately, 26 Americans (mostly suspected CIA agents) and nine Italians were indicted. On November 4, 2009, an Italian judge convicted (in absentia) 23 of the Americans, including a U.S. Air Force (USAF) colonel. Two of the Italians were also convicted in person.

Aafia Siddiqui
The defense for Aafia Siddiqui, who was tried in New York City, alleged that she was held and tortured in a secret US facility at Bagram for several years. Aafia's case gained notoriety due to Yvonne Ridley's allegations in her book, The Grey Lady of Bagram.

The trial began in January 2010 and lasted 14 days, with the jury deliberating for three days before reaching a verdict. On February 3, 2010, she was found guilty of two counts of attempted murder, armed assault, using and carrying a firearm, and three counts of assault on U.S. officers and employees. Siddiqui was sentenced to 86 years in prison on September 23, 2010, following a hearing in which she testified.

Suspected black sites


An estimated 50 prisons have been used to hold detainees in 28 countries, in addition to at least 25 more prisons in Afghanistan and 20 in Iraq. It is estimated that the U.S. has also used 17 ships as floating prisons since 2001, bringing the total estimated number of prisons operated by the U.S. and/or its allies to house alleged terrorist suspects since 2001 to more than 100.

Countries that held suspects on behalf of the U.S. include Algeria, Azerbaijan, Bosnia, Djibouti, Egypt, Ethiopia, Gambia, Israel, Jordan, Kenya, Kosovo, Libya, Lithuania, Mauritania, Morocco, Pakistan, Poland, Qatar, Romania, Saudi Arabia, Syria, Somalia, South Africa, Thailand, United Kingdom, Uzbekistan, Yemen, and Zambia.

Asia
In Thailand, the Voice of America relay station in Udon Thani was reported to be a black site. Former Prime Minister Thaksin Shinawatra has denied these reports.

In Afghanistan, the prison at Bagram Air Base was initially housed in an abandoned brickmaking factory outside Kabul known as the "Salt Pit", but later moved to the base some time after a young Afghan died of hypothermia after being stripped naked and left chained to a floor. During this period, there were several incidents of torture and prisoner abuse, though they were related to non-secret prisoners, and not the CIA-operated portion of the prison. At some point prior to 2005, the prison was again relocated, this time to an unknown site. Metal containers at Bagram Air Base were reported to be black sites. Some Guantanamo Bay detainees report being tortured in a prison they called "the dark prison", also near Kabul. Also in Afghanistan, Jalalabad and Asadabad have been reported as suspected sites.

Middle East
In Iraq, Abu Ghraib was disclosed as also working as a black site, and was the center of an extensive prisoner abuse scandal. Additionally, Camp Bucca (near Umm Qasr) and Camp Cropper (near the Baghdad International Airport) were reported.

Africa
Some reported sites in Egypt, Libya and Morocco, as well as Djibouti The Temara interrogation centre, five miles outside the Moroccan capital, Rabat, is cited as one such site.

On January 23, 2009, The Guardian reported that the CIA ran a secret detention center in Camp Lemonnier in Djibouti, a former French Foreign Legion base.

Indian Ocean
The U.S. Naval Base in Diego Garcia was reported to be a black site, but UK and U.S. officials initially attempted to suppress these reports. However, it has since been revealed by Time magazine and a "senior American official" source that the isle was indeed used by the U.S. as a secret prison for "war on terror" detainees.

While the revelation is expected to cause considerable embarrassment for both governments, UK officials may face considerable exposure since they had previously quelled public outcry over U.S. detainee abuse by falsely reassuring the public no U.S. detainment camps were housed any on UK bases or territories. The UK may also face liabilities over apparent violations of international treaties.

Europe
Several European countries (particularly the former Soviet satellites and republics) have been accused of and have denied hosting black sites: the Czech Republic, Hungary, Poland, Romania, Armenia, Georgia, Latvia, Bulgaria, Azerbaijan and Kazakhstan. Slovak ministry spokesman Richard Fides said the country had no black sites, but its intelligence service spokesman Vladimir Simko said he would not disclose any information about possible Slovak black sites to the media. EU Justice commissioner Franco Frattini has repeatedly asserted suspension of voting rights for any member state found to have hosted a CIA black site.

The interior minister of Romania, Vasile Blaga, has assured the EU that the Mihail Kogălniceanu Airport was used only as a supply point for equipment, and never for detention, though there have been reports to the contrary. A fax intercepted by the Onyx Swiss interception system, from the Egyptian Foreign Ministry to its London embassy, stated that 23 prisoners were clandestinely interrogated by the U.S. at the base. In 2007, it was disclosed by Dick Marty (investigator) that the CIA allegedly had secret prisons in Poland and Romania.

There are other reported sites in Ukraine, who denied hosting any such sites, and the Republic of Macedonia.

In June 2008, a New York Times article claimed, citing unnamed CIA officers, that Khalid Sheikh Mohammed was held in a secret facility in Poland near Szymany Airport, about 100 miles north of Warsaw and it was there where he was interrogated and the waterboarding was applied. It is claimed that waterboarding was used about 100 times over a period of two weeks before Khalid Sheikh Mohammed began to cooperate. In September 2008, two anonymous Polish intelligence officers made the claims about facilities being located in Poland in the Polish daily newspaper Dziennik. One of them stated that between 2002 and 2005 the CIA held terror suspects inside a military intelligence training base in Stare Kiejkuty in north-eastern Poland. The officer said only the CIA had access to the isolated zone, which was used because it was a secure site far from major towns and was close to a former military airport. Both Prime Minister Leszek Miller and President Aleksander Kwasniewski knew about the base, the newspaper reported. However, the officer said it was unlikely either man knew if the prisoners were being tortured because the Poles had no control over the Americans' activities. On January 23, 2009, The Guardian reported that the CIA had run black sites at Szymany Airport in Poland, Camp Eagle in Bosnia and Camp Bondsteel in Kosovo. The United States has refused to cooperate with a Polish investigation into the matter, according to the Helsinki Foundation for Human Rights.

In November 2009, reports alleged a black site referred to in The Washington Post's 2005 article had been located in Lithuania. A former riding school in Antaviliai, a village some 25 km from Vilnius, was said to have been converted into a jail by the CIA in 2004. The allegations resulted in a parliamentary inquiry, and Lithuanian President Dalia Grybauskaitė stated that she had "indirect suspicions" about a black site in her country. On December 22, 2009, the parliamentary commission finished its investigation and stated they found no proof that a black site had existed in Lithuania. Valdas Adamkus, a former president of Lithuania, said he is certain that no alleged terrorists were ever detained on Lithuanian territory.

Mobile sites

 * U.S. warship USS Bataan (LHD-5)  - By definition as a U.S. military vessel, this is not a "black site" as defined above. However, it has been used by the United States military as a temporary initial interrogation site (after which, prisoners are then transferred to other facilities, possibly including black sites).
 * N221SG a Learjet 35
 * N44982 a Gulfstream V (also known as N379P)
 * N8068V a Gulfstream V
 * N4476S a Boeing Business Jet
 * On May 31, 2008, The Guardian reported that the human rights group Reprieve said up to seventeen US Naval vessels may have been used to covertly hold captives.  In addition to the USS Bataan The Guardian named: USS Peleliu and the USS Ashland, USNS Stockham, USNS Watson, USNS Watkins, USNS Sister, USNS Charlton, USNS Pomeroy, USNS Red Cloud, USNS Soderman, and USNS Dahl; MV PFC William B Baugh, MV Alex Bonnyman, MV Franklin J Phillips, MV Louis J Huage Jr and MV James Anderson Jr.  The Ashland was stationed off the coast of Somalia, in 2007, and, Reprieve expressed concern it had been used as a receiving ship for up to 100 captives taken in East Africa.

The Washington Post December 2002
The Washington Post on December 26, 2002, reported about a secret CIA prison in one corner of Bagram Air Force Base (Afghanistan) consisting of metal shipping containers. On March 14, 2004, The Guardian reported that three British citizens were held captive in a secret section (Camp Echo) of the Guantánamo Bay complex. Several other articles reported the retention of ghost detainees by the CIA, alongside the other official "enemy combatants". However, it was the revelations of the Washington Post, in a November 2, 2005, article, that would start the scandal. (below)

Human Rights Watch March 2004 report
A report by the human rights organization Human Rights Watch, entitled "Enduring Freedom - Abuses by US Forces in Afghanistan", states that the CIA has operated in Afghanistan since September, 2001; maintaining a large facility in the Ariana Chowk neighborhood of Kabul and a detention and interrogation facility at the Bagram airbase.

Village March 2005 report
In the 26 February-4 March 2005, edition of Ireland's Village magazine, an article titled "Abductions via Shannon" claimed that Dublin and Shannon airports in Ireland were "used by the CIA to abduct suspects in its 'war on terror'". The article went on to state that a Boeing 737 (registration number N313P, later reregistered N4476S) "was routed through Shannon and Dublin on fourteen occasions from 1 January 2003 to the end of 2004. This is according to the flight log of the aircraft obtained from Washington, D.C., by Village. Destinations included Estonia (1/11/03); Larnaca, Salé, Kabul, Palma, Skopje, Baghdad, (all 16 January 2004); Marka (10 May 2004 and 13 June 2004). Other flights began in places such as Dubai (2 June 2003 and 30 December 2003), Mitiga (29 October 2003 and 27 April 2004), Baghdad (2003) and Marka (8 February 2004, 4 March 2004, 10 May 2004), all of which ended in Washington, D.C..

According to the article, the same aircraft landed in Guantanamo Bay on September 23, 2003, "having travelled from Kabul to Szymany (Poland), Mihail Kogălniceanu (Romania) and Salé (Morocco)". It had been used "in connection with the abduction in Skopje, Republic of Macedonia, of Khalid El-Masri, a German citizen of Lebanese descent, on 31 December 2003, and his transport to a US detention centre in Afghanistan on 23 January 2004".

In the article, it was noted that the aircraft's registration showed it as being owned by Premier Executive Transport Services, based in Massachusetts, though as of February 2005 it was listed as being owned by Keeler and Tate Management, Reno, Nevada (US). On the day of registration transference, a Gulfstream V jet (number N8068V) used in the same activities, was transferred from Premier Executive Transport Services to a company called Baynard Foreign Marketing.

Washington Post November 2005 article
A story by reporter Dana Priest published in The Washington Post of November 2, 2005, reported: "The CIA has been hiding and interrogating some of its most important alleged al Qaeda captives at a Soviet-era compound in Eastern Europe, according to U.S. and foreign officials familiar with the arrangement." According to current and former intelligence officials and diplomats, there is a network of foreign prisons that includes or has included sites in several European democracies, Thailand, Afghanistan, and a small portion of the Guantánamo Bay prison in Cuba - this network has been labeled by Amnesty International as "The Gulag Archipelago", in a clear reference to the novel of the same name by Russian writer and activist Aleksandr Solzhenitsyn.

The reporting of the secret prisons was heavily criticized by members and former members of the Bush Administration. However, Priest states no one in the administration requested that the Washington Post not print the story. Rather they asked they not publish the names of the countries in which the prisons are located. "The Post has not identified the East European countries involved in the secret program at the request of senior U.S. officials who argued that the disclosure could disrupt counter-terrorism efforts".

Human Rights Watch's report
On November 3, 2005, Tom Malinowski of the New York-based Human Rights Watch cited circumstantial evidence pointing to Poland and Romania hosting CIA-operated covert prisons. Flight records obtained by the group documented the Boeing 737 'N4476S' leased by the CIA for transporting prisoners leaving Kabul and making stops in Poland and Romania before continuing on to Morocco, and finally Guantánamo Bay in Cuba. Such flight patterns might corroborate the claims of government officials that prisoners are grouped into different classes being deposited in different locations. Malinowski's comments prompted quick denials by both Polish and Romanian government officials as well as sparking the concern of the International Committee of the Red Cross ("ICRC"), who called for access to all foreign terrorism suspects held by the United States.

The accusation that several EU members may have allowed the United States to hold, imprison or torture detainees on their soil has been a subject of controversy in the European body, who announced in November 2005 that any country found to be complicit could lose their right to vote in the council.

On November 8, 2005, rights group Amnesty International provided the first comprehensive testimony from former inmates of the CIA black sites. The report, which documented the cases of three Yemeni nationals, was the first to describe the conditions in black site detention in detail. In a subsequent report, in April 2006, Amnesty International used flight records and other information to locate the black site in Eastern Europe or Central Asia.
 * Amnesty International November 2005 report

BBC December 2006 report
On 28 December 2006, the BBC reported that during 2003, a well-known CIA Gulfstream V aircraft implicated in extraordinary renditions, N379P, had on several occasions landed at the Polish airbase of Szymany. The airport manager said that airport officials were told to keep away from the aircraft, which parked at the far end of the runway and frequently kept their engines running. Vans from a nearby intelligence base (Stare Kiejkuty) met the aircraft, stayed for a short while and then drove off. Landing fees were paid in cash, with the invoices made out to "probably fake" American companies.

New Yorker August 2007 article
An August 13, 2007, story by Jane Mayer in The New Yorker reported that the CIA has operated "black site" secret prisons by the direct Presidential order of George W. Bush since shortly after 9/11, and that extreme psychological interrogation measures based at least partially on the Vietnam-era Phoenix Program were used on detainees. These included sensory deprivation, sleep deprivation, keeping prisoners naked indefinitely and photographing them naked to degrade and humiliate them, and forcibly administering drugs by suppositories to further break down their dignity. According to Mayer's report, CIA officers have taken out professional liability insurance, fearing that they could be criminally prosecuted if what they have already done became public knowledge.

September 2007 media reports to present
On September 14, 2007, The Washington Post reported that members of the Senate Select Committee on Intelligence had requested the withdrawal of the nomination of John A. Rizzo - a career CIA lawyer - for the position of general counsel, due to concerns about his support for Bush administration legal doctrines permitting "enhanced interrogation" of terrorism detainees in CIA custody.

On October 4, 2007, The New York Times reported that, shortly after Alberto Gonzales became Attorney General in February 2005, the Justice Department issued a secret opinion which for the first time provided CIA explicit authorization to barrage terror suspects with a combination of painful physical and psychological tactics, including head-slapping, simulated drowning and frigid temperatures. This was in direct opposition to a public legal opinion issued in December 2004 that declared torture "abhorrent". Gonzales reportedly approved the legal memorandum on "combined effects" over the objections of James B. Comey, the outgoing deputy attorney general, who told colleagues at the Justice Department that they would all be "ashamed" when the world eventually learned of it. According to the Times report, the 2005 Justice Department opinions remain in effect, and their legal conclusions have been confirmed by several more recent memorandums.

Patrick Leahy and John Conyers, chairmen of the respective Senate and House Judiciary Committees, requested that the Justice Department turn over documents related to the secret February 2005 legal opinion to their committees for review. The chairman of the Senate Intelligence Committee, John D. Rockefeller IV, wrote to acting attorney general Peter D. Keisler, asking for copies of all opinions on interrogation since 2004. "I find it unfathomable that the committee tasked with oversight of the C.I.A.'s detention and interrogation program would be provided more information by The New York Times than by the Department of Justice", Rockefeller's letter read in part. On October 5, 2007, President George W. Bush responded, saying "This government does not torture people. You know, we stick to U.S. law and our international obligations." Bush said that the interrogation techniques "have been fully disclosed to appropriate members of Congress".

On October 11, 2007, The New York Times reported that Hayden had ordered an unusual internal inquiry into the work of the agency's inspector general, John L. Helgerson, whose aggressive investigations of the CIA's detention and interrogation programs and other matters have created resentment among agency operatives. The inquiry is reportedly being overseen by Robert L. Deitz, a lawyer who served as general counsel at the National Security Agency when Hayden ran it, and also includes Michael Morrell, the agency's associate deputy director.

A report by Helgerson's office completed in the spring of 2004 warned that some CIA-approved interrogation procedures appeared to constitute cruel, inhuman and degrading treatment, as defined by the international Convention Against Torture. Some of the inspector general's work on detention issues was conducted by Mary O. McCarthy, who was fired from the agency in 2006 after being accused of leaking classified information. Helgerson's office is reportedly nearing completion on a number of inquiries into CIA detention, interrogation, and renditions. Members of the House and Senate intelligence committees expressed concern about the inquiry, saying that it could undermine the inspector general's role as independent watchdog. Senator Ron Wyden (D–Oregon) said he was sending a letter to Mike McConnell, the director of national intelligence, asking him to instruct Hayden to drop the inquiry.

In an October 30, 2007, address to the Chicago Council on Global Affairs, Hayden defended the agency's interrogation methods, saying, "Our programs are as lawful as they are valuable." Asked a question about waterboarding, Hayden mentioned attorney general nominee Michael Mukasey, saying, "Judge Mukasey cannot nor can I answer your question in the abstract. I need to understand the totality of the circumstances in which this question is being posed before I can give you an answer."

On December 6, 2007, the CIA admitted that it had destroyed videotapes recordings of CIA interrogations of terrorism suspects involving harsh interrogation techniques, tapes which critics suggest may have documented the use of torture by the CIA, such as waterboarding. The tapes were made in 2002 as part of a secret detention and interrogation program, and were destroyed in November 2005. The reason cited for the destruction of the tapes was that the tapes posed a security risk for the interrogators shown on the tapes. Yet the department also stated that the tapes "had no more intelligence value and were not relevant to any inquiries". In response, Senate Armed Services Committee Chairman Carl Levin (D-Michigan) stated: "You'd have to burn every document at the CIA that has the identity of an agent on it under that theory." Other Democrats in Congress also made public statements of outrage about the destruction of the tapes, suggesting that a violation of law had occurred.

European investigations
After a media and public outcry in Europe concerning headlines about "secret CIA prisons" in Poland and other US allies, the EU through its Committee on Legal Affairs investigated whether any of its members, especially Poland, the Czech Republic or Romania had any of these "secret CIA prisons". After an investigation by the EU Committee on Legal Affairs and Human Rights, the EU determined that it could not find any of these prisons. In fact, they could not prove if they had ever existed at all. To quote the report, "At this stage of the investigations, there is no formal, irrefutable evidence of the existence of secret CIA detention centres in Romania, Poland or any other country. Nevertheless, there are many indications from various sources which must be considered reliable, justifying the continuation of the analytical and investigative work."

Nonetheless, the CIA's alleged programme prompted several official investigations in Europe into the existence of such secret detentions and unlawful inter-state transfers involving Council of Europe member states. A June 2006 report from the Council of Europe estimated 100 people had been kidnapped by the CIA on EU territory (with the cooperation of Council of Europe members), and rendered to other countries, often after having transited through secret detention centres ("black sites") used by the CIA, some located in Europe. According to the separate European Parliament report of February 2007, the CIA has conducted 1,245 flights, many of them to destinations where suspects could face torture, in violation of article 3 of the United Nations Convention Against Torture.

Spanish investigations
In November 2005, El País reported that CIA planes had landed in the Canary Islands and in Palma de Mallorca. An attorney opened up an investigation concerning these landings which, according to Madrid, were made without official knowledge, thus being a breach of national sovereignty.

French investigations
The prosecutor of Bobigny court, in France, opened up an investigation in order "to verify the presence in Le Bourget Airport, on July 20, 2005, of the plane numbered N50BH". This instruction was opened following a complaint deposed in December 2005 by the Ligue des droits de l'homme (LDH) NGO ("Human Rights League") and the International Federation of Human Rights Leagues (FIDH) NGO on charges of "arbitrary detention", "crime of torture" and "non-respect of the rights of war prisoners". It has as objective to determine if the plane was used to transport CIA prisoners to Guantanamo Bay detainment camp and if the French authorities had knowledge of this stop. However, the lawyer defending the LDH declared that he was surprised that the judicial investigation was only opened on January 20, 2006, and that no verifications had been done before.

On December 2, 2005, conservative newspaper Le Figaro had revealed the existence of two CIA planes that had landed in France, suspected of transporting CIA prisoners. But the instruction concerned only N50BH, which was a Gulfstream III, which would have landed at Le Bourget on July 20, 2005, coming from Oslo, Norway. The other suspected aircraft would have landed in Brest on March 31, 2002. It is investigated by the Canadian authorities, as it would have been flying from St. John's, Newfoundland and Labrador in Canada, via Keflavík in Iceland before going to Turkey.

Portuguese investigations
On February 5, 2007, Portuguese general prosecutor Cândida Almeida, head of the Central Investigation and Penal Action Department (DCIAP), announced an investigation of "torture or inhuman and cruel treatment", prompted by allegations of "illegal activities and serious human rights violations" made by MEP Ana Gomes to the attorney general, Pinto Monteiro, on January 26, 2007.

Gomes was highly critical of the Portuguese government's reluctance to comply with the European Parliament Commission investigation into the CIA flights, leading to tensions with Foreign Minister Luís Amado, a member of her party. She said she had no doubt that illegal flights were frequently permitted during the Durão Barroso (2002–2004) and Santana Lopes (2004–2005) governments, and that "during the [present Socialist] government of José Sócrates, 24 flights which passed through Portuguese territory" are documented. She expressed satisfaction with the opening of the investigation, but emphasized that she had always said a parliamentary inquiry would also be necessary.

Visão magazine journalist Rui Costa Pinto also testified before the DCIAP. He had written an article, rejected by the magazine, about flights passing through Lajes Field in the Azores, a Portuguese airbase used by the US Air Force. Costa Pinto wrote a book about his investigation.

Approximately 150 CIA flights have been identified as having flown through Portugal.

Polish investigations
In January 2012, Poland's Prosecutor General's office initiated investigative proceedings against Zbigniew Siemiątkowski, the former Polish intelligence chief. Siemiątkowski is charged with facilitating the alleged CIA detention operation in Poland, where foreign suspects may have been tortured in the context of the War on Terror. The alleged constitutional and international law trespasses took place when Leszek Miller, presently member of parliament and leader of the Democratic Left Alliance, was Prime Minister (2001–2004), and he may also be subjected to future legal action (a trial before the State Tribunal of the Republic of Poland).

The future robustness of the highly secret investigation, in progress since 2008, may however be in some doubt. According to the leading Polish newspaper Gazeta Wyborcza, soon after Siemiątkowski was charged by the prosecutors in Warsaw, the case was transferred and is now expected to be handled by a different prosecutorial team in Cracow. The United States authorities have refused to cooperate with the investigation and the turning over of the relevant documents to the prosecution by the unwilling Intelligence Agency was forced only after the statutory intervention of the First President of the Supreme Court of Poland.

Abu Zubaydah and Abd al-Rahim al-Nashiri are said to have been held and subjected to physical punishments at the Stare Kiejkuty intelligence base in northeastern Poland.

Other European investigations
The European Union (EU) as well as the Council of Europe pledged to investigate the allegations. On November 25, 2005, the lead investigator for the Council of Europe, Swiss lawmaker Dick Marty announced that he had obtained latitude and longitude coordinates for suspected black sites, and he was planning to use satellite imagery over the last several years as part of his investigation. On November 28, 2005, EU Justice Commissioner Franco Frattini asserted that any EU country which had operated a secret prison would have its voting rights suspended. On 13 December 2005 Dick Marty, investigating illegal CIA activity in Europe on behalf of the Council of Europe in Strasbourg, reported evidence that "individuals had been abducted and transferred to other countries without respect for any legal standards". His investigation has found that no evidence exists establishing the existence of secret CIA prisons in Europe, but added that it was "highly unlikely" that European governments were unaware of the American program of renditions. However, Marty's interim report, which was based largely on a compendium of press clippings has been harshly criticised by the governments of various EU member states. The preliminary report declared that it was "highly unlikely that European governments, or at least their intelligence services, were unaware" of the CIA kidnapping of a "hundred" persons on European territory and their subsequent rendition to countries where they may be tortured.

On April 21, 2006, the New York Times reported that European investigators said they had not been able to find conclusive evidence of the existence of European black sites.

On 27 June 2007, the Parliamentary Assembly of the Council of Europe voted on Resolution 1562 and Recommendation 1801 backing the conclusions of the report by Dick Marty. The Assembly declared that it was established with a high degree of probability that secret detention centres had been operated by the CIA under the High Value Detainee (HVD) program for some years in Poland and Romania.

The Onyx-intercepted fax
In its edition of January 8, 2006, the Swiss newspaper Sonntagsblick published a document intercepted on November 10 by the Swiss Onyx interception system (similar to the UKUSA's ECHELON system). Purportedly sent by the Egyptian embassy in London to foreign minister Ahmed Aboul Gheit, the document states that 23 Iraqi and Afghan citizens were interrogated at Mihail Kogălniceanu base near Constanţa, Romania. According to the same document, similar interrogation centers exist in Bulgaria, Kosovo, the Republic of Macedonia, and Ukraine.

The Egyptian Foreign Ministry later explained that the intercepted fax was merely a review of the Romanian press done by the Egyptian Embassy in Bucharest. It probably referred to a statement by controversial Senator and Great Romania party leader Corneliu Vadim Tudor.

The Swiss government did not officially confirm the existence of the report, but started a judiciary procedure for leakage of secret documents against the newspaper on 9 January 2006.

The European Parliament's February 14, 2007, report
The European Parliament's report, adopted by a large majority (382 MEPs voting in favour, 256 against and 74 abstaining) passed on February 14, 2007, concludes that many European countries tolerated illegal actions of the CIA including secret flights over their territories. The countries named were: Austria, Belgium, Cyprus, Denmark, Germany, Greece, Ireland, Italy, Poland, Portugal, Romania, Spain, Sweden and the United Kingdom. The report: "denounces the lack of co-operation of many member states and of the Council of the European Union with the investigation; Regrets that European countries have been relinquishing control over their airspace and airports by turning a blind eye or admitting flights operated by the CIA which, on some occasions, were being used for illegal transportation of detainees; Calls for the closure of [the US military detention mission in] Guantanamo and for European countries immediately to seek the return of their citizens and residents who are being held illegally by the US authorities; Considers that all European countries should initiate independent investigations into all stopovers by civilian aircraft [hired by] the CIA; Urges that a ban or system of inspections be introduced for all CIA-operated aircraft known to have been involved in extraordinary rendition."

The report criticized a number of European countries (including Austria, Italy, Poland, Portugal and the UK) for their "unwillingness to co-operate" with investigators and the action of secret services for lack of cooperation with the Parliaments' investigators and acceptal of the illegal abductions. The European Parliament voted a resolution condemning member states which accepted or ignore the practice. According to the report, the CIA had operated 1,245 flights, many of them to destinations where suspects could face torture. The Parliament also called for the creation of an independent investigation commission and the closure of Guantanamo. According to Giovanni Fava (Socialist Party), who drafted the document, there was a "strong possibility" that the intelligence obtained under the extraordinary rendition illegal program had been passed on to EU governments who were aware of how it was obtained. The report also uncovered the use of secret detention facilities used in Europe, including Romania and Poland. The report defines extraordinary renditions as instances where "an individual suspected of involvement in terrorism is illegally abducted, arrested and/or transferred into the custody of US officials and/or transported to another country for interrogation which, in the majority of cases involves incommunicado detention and torture".

Obama administration
On January 22, 2009, US President Barack Obama signed an executive order requiring the CIA to use only the 19 interrogation methods outlined in the United States Army Field Manual "unless the Attorney General with appropriate consultation provides further guidance". The order also provided that "The CIA shall close as expeditiously as possible any detention facilities that it currently operates and shall not operate any such detention facility in the future."

On March 5, 2009, Bloomberg News reported that the United States Senate intelligence committee was beginning a one-year inquiry in the CIA's detention program.

In April, 2009, CIA director Leon Panetta announced that the "CIA no longer operates detention facilities or black sites", in a letter to staff and that "[r]emaining sites would be decommissioned". He also announced that the CIA was no longer allowing outside "contractors" to carry out interrogations and that the CIA no longer employed controversial "harsh interrogation techniques". Panetta informed his fellow employees that the CIA would only use interrogation techniques authorized in the US Army interrogation manual, and that any individuals taken into custody by the CIA would only be held briefly, for the time necessary to transfer them to the custody of authorities in their home countries, or the custody of another US agency.

In 2011, the Obama administration admitted that it had been holding a Somali prisoner for two months aboard a US Navy ship at sea for interrogation.