NEW YORK - A cache of previously secret military documents about detainees at Guantanamo Bay prison in Cuba have revealed that the US believed many of those held at the notorious detention facility were innocent or only low-level operatives. The dossiers, obtained by The New York Times and several other news organizations, reveal analysis of all 779 people ever held at the facility. They show that about 220 were classed as dangerous terrorists, but 150 were innocent Afghans and Pakistanis. Another 380 people were deemed to be low-ranking foot soldiers. 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 Pentagon's 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 U.S. and its allies in the future. The files are part of thousands of pages of classified information that was leaked last year to the anti-secrecy website Wikileaks. They were made available to the New York Times by another source, on condition of anonymity. These intelligence summaries and assessments - which date back as far as 2002 and run until the beginning of 2009 - pull back the curtain on a sometimes chaotic process as officials at Guantanamo tried to determine whether detainees continue to be held, released to a third country, or prosecuted for terrorism and other crimes, the newspaper said. 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 Laden's personal English translator. Abd al-Rahim al-Nashiri, the suspected plotter of the U.S.S Cole attack in Yemen, reported directly to Osama bin Laden, according to the documents. And in at least two cases, the documents show that Guantanamo officials were aware that they had innocent men in captivity and even put that in writing in their prison files, and yet it took months to return them to their home countries. 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. "Both Administrations have made the protection of American citizens the top priority, and we are concerned that the disclosure of these documents could be damaging to those efforts." The statement said it was "unfortunate" The New York Times and other news organizations 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 Department's special envoy in charge of negotiating the closure of the Guantanamo facility Meanwhile, U.S. 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 U.S. and its allies. But four years ago, the U.S. released him to the Libyan government anyway. U.S. 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. The documents say he was forced to leave Sudan sometime in 1997. From there he went directly to the tribal regions of Pakistan where he allegedly received additional training with al-Qaeda. U.S. intelligence reports in the file say his name appeared on a hard drive that listed al-Qaeda employees and their monthly wages. That's significant because most al-Qaeda's ranks tend to be volunteers - people on the payroll are considered more than just lowly foot soldiers. Now that Qumu has turned up in Libya, U.S. intelligence is trying to figure out if he still has those al-Qaida 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. 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. Prisoners who especially worried counterterrorism officials included some accused of being assassins for Al Qaeda, operatives for a canceled suicide mission and detainees who vowed to their interrogators that they would wreak revenge against America, according to the newspaper. PERVEZ MUSHARRAF It said the military analysts files provide new details about the most infamous of their prisoners, Khalid Shaikh Mohammed, the planner of the Sept. 11, 2001, attacks. Sometime around March 2002, he ordered a former Baltimore resident to don a suicide bomb vest and carry out a martyrdom attack against former Pakistan president Pervez Musharraf according to the documents. But when the man, Majid Khan, got to the Pakistani mosque that he had been told Mr. Musharraf would visit, the assignment turned out to be just a test of his willingness to die for the cause. The documents are largely silent about the use of the harsh interrogation tactics at Guantanamo that drew global condemnation, the newspaper reported. President Barack Obama pledged two years ago to close the prison at U.S. 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 administration's Guantanamo review panel, established in January 2009, had made its own assessments. "The assessments of the Guantanamo Review Task Force have not been compromised to Wikileaks. Thus, any given DAB (Detainee Assessment Briefs) illegally obtained and released by WikiLeaks may or may not represent the current view of a given detainee," the statement said. This was the latest batch of secret U.S. documents dumped by WikiLeaks, which had previously released classified Pentagon reports on the wars in Afghanistan and Iraq and 250,000 State Department cables. Bradley Manning, a 23-year-old U.S. soldier accused of leaking secret documents to WikiLeaks has been detained since May of last year. The Guantanamo detention camp was opened to house prisoners captured in the U.S.-led Afghan war launched by President George W. Bush soon after the September 11, 2001, attacks on the United States.