The CIA has been accused of covering up the torture of two top Al-Qaeda terror suspects after it emerged that White House and justice department officials and senior congressmen warned it against destroying hundreds of hours of videotape of the interrogations in 2003.

The tapes were destroyed in November 2005, the month in which The Washington Post exposed the CIA’s imprisonment of suspected terrorists at “black sites”. Last night the justice department and the CIA’s internal watchdog launched an investigation.

The tapes show the interrogations of Abu Zubaydah and Abd al-Rahim al-Nashiri, who are now held in Guantanamo Bay. Zubaydah is believed to have been “waterboarded”, a technique that induces panic by simulating drowning, while al-Nashiri has complained that he was extensively tortured.

Harriet Miers, the White House counsel for President George W Bush, told CIA officials she opposed the destruction of the tapes, according to Bush administration sources. Porter Goss, who went on to become director of the CIA in 2004, also warned against their destruction when he was a senior congressman in charge of the House intelligence committee.

The destruction of the tapes occurred on Goss’s watch, but it appears he was not warned in advance by Jose Rodriguez, the head of the agency’s clandestine service. The existence of the tapes was kept secret from members of the September 11 commission, which had asked for all material relating to detainees.

Lee Hamilton, the co-chairman of the September 11 commission, said: “It certainly raises a suspicion of a cover-up, of activities they’re not proud of . . . activities they might even think are criminal.” The CIA had clearly obstructed the inquiry, Hamilton added.

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