The CIA destroyed video evidence of the coercive interrogation of al-Qaida operatives held under its secret rendition programme in order to shield agents from prosecution, it was revealed yesterday.

The decision to destroy two videotapes documenting the use of waterboarding against Abu Zubaydah and another high-value al-Qaida detainee was made in November 2005 - as American media were just beginning to focus on the existence of the secret CIA prison network.

"The tapes posed a serious security risk," the CIA's director, Michael Hayden, told agency employees in a statement yesterday. "Were they ever to leak, they would permit identification of your CIA colleagues who had served in the programme, exposing them and their families to retaliation from al-Qaida and its sympathisers."

Hayden's message to CIA employees went out a day after he learned that the New York Times planned to publish an article today about destruction of the videotapes.

The revelation is bound to reignite debate in Congress about the use of torture in the war on terror. But far more seriously for the Bush administration, it raises the prospect that the CIA withheld information from and obstructed the work of the commission investigating the September 11 attacks as well as lawyers for Zacarias Moussaoui, the so-called 11th hijacker. Officials from the September 11 commission told the New York Times yesterday they had formally requested from the CIA evidence of interrogations, and had been informed that all materials had been handed over.

The Washington Post, which also carried a story on its website yesterday about the destroyed videotapes, reported that the order to destroy the tapes came from Jose Rodriguez Jr, then the director of the CIA's clandestine operations.

The leaders of the house and Senate intelligence committees - which were then under Republican control - were aware of the existence of the footage and the CIA's decision to destroy the material, Hayden said in his memo. However, Democratic committee members who had long demanded that such interrogations be videotaped, were not made aware of the existence of the tapes, the Times reported.

Hayden said the interrogations were filmed in 2002 after George Bush authorised the use of harsh interrogation, including the controversial practice of controlled drowning, known as waterboarding, against al-Qaida suspects.

"The agency was determined that it proceed in accord with established legal and policy guidelines," Hayden wrote. "So, on its own, CIA began to videotape interrogations."

However, the CIA soon discontinued the practice, and it is believed that only two detainees were filmed while undergoing interrogation. It has long been believed that Abu Zubaydah, a Saudi believed to be a close associated of Osama bin Laden, was subjected to harsh treatment following his capture in Pakistan in March 2002.

The footage would have clarified what practices such as waterboarding and sleep deprivation - both of which a gravely wounded Abu Zubaydah was subjected to - involve.