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The Pakistani spy agency, the Inter-Service Intelligence, was considered by the United States to be on par with terror groups such as al-Qaeda and the Taliban, according to a slew of “secret” government documents on detainees in the Guantanamo Bay prison.

According to the documents, released on Sunday by newspapers such as the Guardian, “U.S. authorities describe the main Pakistani intelligence service as a terrorist organisation.” Analysts’ notes based on the interrogation of the detainees list numerous examples of the ISI “supporting, co-ordinating and protecting insurgents fighting coalition forces in Afghanistan, or even assisting al-Qaeda.”

One case, backed up by files published publicly by the Guardian, relates to “veteran militant” Harun Shirzad al-Afghani, who was said to have attended a meeting in August 2006 at which Pakistani military and intelligence officials joined senior figures in the Taliban, al-Qaida, the Lashkar-e-Taiba as well.

According to the official memo, the meeting that al-Afghani attended was to discuss operations in Afghanistan against coalition forces and it ended with a decision by the insurgent factions “to increase terrorist operations in the Kapisa, Kunar, Laghman and Nangarhar provinces [of Afghanistan], including suicide bombings, mines, and assassinations.”

The Guardian further published another Guantanamo Bay prison official file on a “high-profile Afghan religious and political leader,” which made reference to ISI operations in the eastern province of Kunar during 2002. According to the memo in question those operations were “designed to destabilise the new Afghan government under Hamid Karzai, who had been installed as interim President by the U.S.-led coalition.”

The memo reportedly said, “In January 2002 ISI financed the activities of several factions … in Kunar… in order to destabilise the Afghan [government]. In March 2002 [the ISI] reportedly provided $12,000… to finance military operations against the new government.”

While the revelations outlined in the Guantanamo Bay prison files are likely to further weaken the rocky relationship between the U.S. and Pakistan, some of the memos also suggested that “rogue elements” within the ISI sometimes acted without the official sanction of the Pakistani state.

In particular one memo describes how “rogue factions from the ISI have routinely pursued private interests and acted against the stated policy of the government of Pakistan,” and these elements have also “had sympathies for and provided support to anti-coalition militia.”

Yet the memos also show the U.S.-Pakistan relationship to be a double-edged sword, especially as they supply evidence showing “extensive” U.S.-ISI collaboration in intelligence gathering. Specifically the memos suggest that many of those transferred to Guantánamo Bay, including senior al-Qaida figures such as Khaled Sheikh Mohammed, “were arrested with Pakistani help or turned over to American authorities by Pakistani intelligence services.”

The cache of files on Guantanamo Bay prison were said to have been provided to European newspapers by the New York Times. The NYT, however, did not confirm that it had obtained the 759 "detainee assessment" dossiers written between 2002 and 2009 from WikiLeaks, the whistleblower website.

WikiLeaks has been the primary source of a vast collection of government documents, including some pertaining to U.S. military engagement in Iraq and Afghanistan and others relating to confidential cables of the U.S. State Department.