US President George W Bush has said he has "no recollection" of the existence of video tapes of CIA interrogations and the plan to destroy them.
President Bush insists that the US does not use torture
The CIA says it wiped two tapes of interrogations of al-Qaeda suspects to protect the identities of its agents.
But human rights groups accuse it of destroying evidence of practices that may be tantamount to torture.
A US Senate committee has promised a thorough investigation into the history of the making and wiping of the tapes.
Mr Bush continued to have confidence in CIA Director Michael Hayden, White House spokeswoman Dana Perino said.
The president "did not remember" being told of the tapes prior to Thursday, she said.
The CIA confirmed on Thursday allegations in the New York Times that two tapes were destroyed in 2005.
Officials feared the tapes could have raised doubts about the legality of the CIA's techniques, the newspaper says.
'CIA ENHANCED INTERROGATION TECHNIQUES'
Water boarding: prisoner bound to a board with feet raised, and cellophane wrapped round his head. Water is poured onto his face and is said to produce a fear of drowning
Cold cell: prisoner made to stand naked in a cold, though not freezing, cell and doused with water
Standing: Prisoners stand for 40 hours and more, shackled to the floor
Belly slap: a hard slap to the stomach with an open hand. This is designed to be painful but not to cause injury
Source: Described to ABC News by un-named CIA agents in 2005
The Senate Intelligence Committee chairman, John Rockefeller, a Democrat, called for a thorough investigation into the tapes and their destruction.
Gen Hayden said House and Senate intelligence committee members had been informed of the tapes and the decision to wipe them.
Jane Harman, a senior Democrat who was on the House Intelligence Committee at the time, said she had been informed of the decision, but was opposed to it.
"I told the CIA that destroying videotapes of interrogations was a bad idea and urged them in writing not to do it," she told the Associated Press.
Pete Hoekstra, a Republican who was chairman of the House Intelligence Committee at the time, told the news agency he did not recall being briefed on the matter at all.
Separately, Assistant Senate Democratic Leader Dick Durbin asked the Attorney General to request an investigation into whether the CIA broke obstruction-of-justice laws by destroying the footage.
The CIA revelation has drawn criticism from civil liberties and human rights groups.
Jennifer Daskal, senior counsel with Human Rights Watch, said the wiping of the tapes was "destruction of evidence", and described the reasons given by the CIA as "disingenuous".
The American Civil Liberties Union accused the agency of showing an utter disregard for the law.
"The destruction of these tapes appears to be a part of an extensive, long-term pattern of misusing executive authority to insulate individuals from criminal prosecution for torture and abuse," an ACLU statement said.
Gen Hayden explained why the footage was destroyed in an internal memo sent to CIA employees and obtained by the Associated Press.
He said the CIA had begun taping interrogations as an internal check in 2002 and decided to delete the videos because they no longer had "intelligence value" and posed a security risk.
"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-Qaeda and its sympathisers," he said.
The BBC's Jonathan Beale in Washington says the news is likely to trigger more questions about the interrogation techniques used by the CIA and whether they amounted to torture.
After the 9/11 terrorist attacks on the US, President Bush authorised the use of "harsh techniques" in the interrogation of suspected terrorists.
Michael Hayden wrote to all CIA employees about the tapes
According to our correspondent, those techniques are alleged to have included water-boarding, a method in which a suspect is made to feel he is drowning.
Human rights groups say that water-boarding - and other techniques allegedly used by the CIA - can be defined as torture under various international treaties to which the US is a signatory.
Gen Hayden says that the CIA's internal watchdogs saw the tapes in 2003 and verified that the techniques used were legal.
The Bush administration has always maintained that it does not allow the use of torture.
The tapes are thought to have shown the interrogation in 2002 of a number of terror suspects, including Abu Zubaydah, who had been a chief recruiter for the al-Qaeda network.