The CIA has for the first time publicly admitted using the controversial method of "waterboarding" on terror suspects.
CIA director Michael Hayden told Congress however that it had only been used on three people, and not at all for the past five years.
He said the technique had been used on high-profile al-Qaeda detainees including Khalid Sheikh Mohammed.
Mr Hayden was speaking as National Intelligence Director Mike McConnell presented his annual threat assessment.
Waterboarding is an interrogation technique in which the detainee is put in fear of drowning.
Some critics describe it as torture and Congress has been debating banning its use by the CIA.
President Bush has threatened to veto such a bill.
Mr Hayden said the CIA had also used waterboarding against two other top al-Qaeda suspects, Abu Zubaydah and Abd al-Rahim al-Nashiri.
He told Congress: "We used it against these three detainees because of the circumstances at the time.
"There was the belief that additional catastrophic attacks against the homeland were inevitable. And we had limited knowledge about al-Qaeda and its workings.
"Those two realities have changed."
In his report, National Intelligence Director Mike McConnell focussed attention on al-Qaeda and its leadership based in the border area between Pakistan and Afghanistan.
"Al-Qaeda remains the pre-eminent threat against the United States, both here at home and abroad," he said.