NEW YORK Amid other blunders, the US military classified Pakistans premium spy agency as a terrorist support entity in 2007 and used association with it as a justification to detain prisoners in Guantanamo Bay, according to leaked documents published on Sunday that are sure to further alienate Pakistan, the frontline ally in the war on terror. One document, given to The New York Times, says detainees who allegedly associated with the Inter-Services Intelligence Directorate may have provided support to al-Qaeda or the Taliban, or engaged in hostilities against US or Coalition forces. The ISI , along with al-Qaeda, Hamas and Hezbollah and Iranian intelligence, are among 32 groups on the list of associated forces, which also includes Egypts Islamic Jihad, headed by al-Qaeda deputy Ayman al-Zawahiri. The document defines an associate force as militant forces and organisations with which al-Qaeda, the al-Qaeda network, or the Taliban has an established working, supportive, or beneficiary relationship for the achievement of common goals. Earlier, the US Joint Chiefs of Staff Chairman Admiral Mike Mullen had said, ISI has a long standing relationship with extremist networks. The document in question, JTF-GTMO Matrix of Threat Indicators for Enemy Combatants, likely dates from 2007 according to its classification code, and is part of a trove of 759 files on detainees held in Guantanamo Bay, the US military prison in Cuba. However, the timing of documents puts a big question mark on its authenticity in the first place. The secret documents were obtained by WikiLeaks and date from between 2002 and 2009, but they were made available to The New York Times from a separate source, the paper said. They reveal that most of the 172 remaining prisoners have been rated as a high risk of posing a threat to the United States and its allies if released without adequate rehabilitation and supervision, the newspaper said. The documents also show about a third of the 600 detainees already sent to other countries were also designated high risk before they were freed or passed to the custody of other governments, the Times said in its report late on Sunday. The dossiers, prepared under the Bush administration, also show the seat-of-the-pants intelligence gathering in war zones that led to the incarcerations of innocent men for years in cases of mistaken identity or simple misfortune, the Times said. The documents are largely silent about the use of the harsh interrogation tactics at Guantanamo that drew global condemnation, the newspaper reported. The Times also said an Obama administration task force set up in January 2009 had reviewed the assessments and, in some cases, come to different conclusions. Thus... the documents published by The Times may not represent the governments current views of detainees at Guantanamo. WikiLeaks previously released classified Pentagon reports on the wars in Afghanistan and Iraq and 250,000 State Department cables. Bradley Manning, a 23-year-old US soldier accused of leaking secret documents to WikiLeaks has been detained since May of last year. The Guardian newspaper has obtained papers that reveal that the US authorities instructed interrogators at Guantanamo Bay to treat those connected with the ISI alongside terrorists associated with organisations such as al-Qaeda, Hamas and Hezbollah. The revelations are bound to strain US-Pakistan relations further, although the papers date back to 2007. Washington Post reported on Monday citing documents accessed by WikiLeaks that some senior al-Qaeda leaders were in Karachi on Sep 11, 2001 and most returned to Afghanistan within a day. The media report said that core al-Qaeda leaders were in Karachi. While one of them was recovering at a hospital from a tonsillectomy and another was buying lab equipment for a biological weapons programme, key al-Qaeda members were watching the scenes from New York and Washington on television. The documents show that just four days after 9/11, al-Qaeda leader Osama bin Laden went to a guesthouse in Afghanistans Kandahar province. For the next three months, bin Laden and his confidant Ayman al Zawahiri travelled by car to several areas in Afghanistan. It was during that time that he delegated control of al-Qaeda to the groups Shura Council. Leaked files revealed the mastermind of the 9/11 attacks warned that al-Qaeda has hidden a nuclear bomb in Europe which will unleash a nuclear hellstorm if Osama bin Laden is captured. The terror group also planned to make a 9/11 style attack on Londons Heathrow airport by crashing a hijacked airliner into one of the terminals, the files showed. Khalid Sheikh Mohammed told Guantanamo Bay interrogators the terror group would detonate the nuclear device if the al-Qaeda chief was captured or killed, according to the classified files released by the WikiLeaks website. Sheikh Mohammed, the self-professed mastermind of the September 11, 2001 attacks on the United States, has been held at Guantanamo since 2006 and is to be tried in a military court at the US naval base on Cuba over the attacks. His nuclear threat was revealed in Britains Daily Telegraph newspaper, one of several media outlets which have published the classified assessments of detainees at Guantanamo. The German weekly Der Spiegel, also citing WikiLeaks, said that Sheikh Mohammed had told his interrogators he had set up two cells for the purpose of attacking Heathrow in 2002. The aim was to seize control of an airliner shortly after take-off from Heathrow, one of the worlds busiest airports, turn it around and crash it into one of the four terminals. According to leaked classified files, the United States held hundreds of inmates who were either totally innocent or low-risk for years and released dozens of high-risk Guantanamo inmates. The new leaks reveal that inmates were held without trial on the basis of often seriously flawed information, such as from mentally ill or otherwise unreliable co-detainees or statements from suspects who had been abused or tortured, The New York Times reported. It said that overall, US military analysts considered only 220 of all the suspects in the George W. Bush-era war on terror ever detained at Guantanamo to be dangerous extremists. Another 380 were deemed to be low-ranking foot soldiers who traveled to Afghanistan or were part of the Taliban, the Telegraph reported. In dozens of cases, senior US commanders were said to have concluded that there was no reason recorded for transfer to Guantanamo Bay. According to a paper, the best-documented case of an abusive interrogation at Guantanamo was the questioning in 2002 and 2003 of Mohammed Qahtani, a Saudi believed to have taken part in plotting the September 11 attacks. Qahtani was leashed like a dog, sexually humiliated and forced to urinate on himself, the paper said. Although publicly released records allege detainee was subject to harsh interrogation techniques in the early stages of detention, Gahtanis file noted, his confessions appear to be true and are corroborated in reporting from other sources. The dossiers show that 150 of the detainees were innocent Afghans and Pakistanis. There are now just over 180 detainees at the US naval base in Cuba. The hundreds of classified documents - marked secret and noforn meaning the information is not to be shared with representatives of other countries - are assessments, interviews and internal memos from the Pentagons Joint Task Force at Guantanamo. The task force was supposed to determine who the detainees were, how they might be connected to terrorism and whether they posed a threat to the US and its allies in the future. Among the findings in the files: A former detainee, Abu Sufian Ibrahim Ahmed Hamuda Bin Qumu, who is believed to be training rebel forces in Libya, has closer ties to al-Qaeda than previously understood publicly. According to his detainee assessment, Qumu allegedly trained at two al-Qaeda camps, fought in Afghanistan against the Soviets and the Northern Alliance, and moved to Sudan with other al-Qaeda members. There is new detail on a senior explosives trainer for al-Qaeda, Tariq Mahmud Ahmad al Sawah, the man who claimed to have designed the prototype for a shoe bomb that failed ignite on a US plane in 2001. He was recommended for release from the prison because of his cooperation with authorities. Shaker Aamer, also known as Sawad al-Madani, and called the professor at Guantanamo, said he had no connection to al-Qaeda. His military assessment says he was Osama bin Ladens personal English translator. Abd al-Rahim al-Nashiri, the suspected plotter of the USS Cole attack in Yemen, reported directly to Osama bin Laden, according to the documents. In an official statement to The New York Times, the Obama Administration defended their system for processing detainees. Both the previous and the current administrations have made every effort to act with the utmost care and diligence in transferring detainees from Guantanamo, the statement said. The statement said it was unfortunate The New York Times and other news organisations are publishing the classified Guantanamo documents. We strongly condemn the leaking of this sensitive information, the statement said. It was signed by Pentagon press secretary Geoff Morrell and Ambassador Dan Fried, the State Departments special envoy in charge of negotiating the closure of the Guantanamo facility Meanwhile, US intelligence sources told National Public Radio (NPR) they have been tracking a former Libyan detainee named Abu Sufian Qumu. He was picked up in Pakistan and arrived in Guantanamo in early 2002. The Libyan government asked for him back in 2007. Guantanamo officials who investigated Qumu at that time thought he posed a future risk to the US and its allies. But four years ago, the US released him to the Libyan government anyway. US intelligence officials now believe Qumu is helping train anti-government forces in Benghazi, Libya. It is unclear whether he is a leader of the rebels or simply joining in the anti-Qaddafi movement. What is certain, is that his secret Guantanamo file shows an association with al-Qaeda that stretches back decades. Now that Qumu has turned up in Libya, US intelligence is trying to figure out if he still has those al-Qaeda connections. Member of Congress are wondering the same thing. During Congressional hearings earlier this month Senator James Inhofe, a Republican, asked Admiral James Stavridis about the presence of al-Qaeda among the rebel forces. In an another revealation, a file about Khalid Shaikh Mohammed says that sometime around March 2002, he ordered a former Baltimore resident to don a suicide bomb vest and carry out a martyrdom attack against then president Pervez Musharraf. But when the man, Majid Khan, got to the mosque that he had been told Musharraf would visit, the assignment turned out to be just a test of his willingness to die for the cause. President Barack Obama pledged two years ago to close the prison at US naval base in Cuba but it remains in legal limbo. Obama administration officials condemned the leaking of the documents but said the material is out of date. Pentagon spokesman Geoff Morrell and State Department envoy Dan Fried said in a joint statement that the administrations Guantanamo review panel, established in January 2009, had made its own assessments.