He vowed to find out who authorised the destruction of the tapes, and why congress was not told about it.
Hayden said since the interrogations were recorded under one of his predecessors, George Tenet, and the tapes were destroyed under another, Porter Goss, he was not able to completely answer all questions.
"Other people in the agency know about this far better than I," he said, and promised the committee he would make those witnesses available.
He says congress was notified in 2003 about the existence of tapes of interrogations of two terrorist suspects in 2002 and the intention to destroy them.
The CIA destroyed the tapes in November of 2005. When congress was notified and in what detail remains unclear.
Multiple investigations have begun into who approved the decision to destroy the tapes and why.
White House 'approval'
The hearing came as a former CIA agent who led the team that interrogated Abu Zubaydah, suspected to be a senior member of al-Qaeda, said that waterboarding was effectively used to get information from him.
Hayden says congress was told in 2003 about
the tapes and the intent to destroy them [AFP]
John Kiriakou, now retired, said the method was approved at the highest levels of the US government.
"This isn't something done willy nilly. This isn't something where an agency officer just wakes up in the morning and decides he's going to carry out an enhanced technique on a prisoner,'' Kiriakou said in a round of television news show appearances.
"This was a policy made at the White House, with concurrence from the national security council and justice department.''
Kiriakou said he had no knowledge that the session was being recorded or that the tapes were subsequently destroyed.
"He [Abu Zubaydah] was able to withstand the waterboarding for quite some time - about 30-35 seconds," Kiriakou said.
"[A] short time afterwards, in [the] next day or so, he told his interrogators that Allah had visited him in his cell at night and told him to co-operate because his co-operation would make it easier on the other brothers who'd been captured.
"From that day on, he answered every question. The threat information he provided disrupted a number of attacks, maybe dozens of attacks."
Waterboarding involves strapping down a prisoner, covering his mouth with plastic or cloth and pouring water over his face so that he inhales water, causing the sensation of drowning.
When asked if the waterboarding broke Abu Zubaydah, Kiriakou said: "I think it did, yes.
"We are Americans and we're better than this and we shouldn't be doing this kind of thing.
"But at the same time, what happens if we don't waterboard a person and we don't get that nugget of information? I would have trouble forgiving myself."
Torture debate
The CIA, under Hayden, banned waterboarding in 2006 and the Bush administration has repeatedly denied authorising torture.
George Bush, the US president, said CIA procedures were safe, lawful and necessary. Human-rights groups say waterboarding is torture.
International law defines torture as "an act by which severe pain or suffering, whether physical or mental, is intentionally inflicted on a person for such purposes as obtaining from him ... information or a confession".
When asked about the use of waterboarding, Dick Cheney, said: "Would you agree a dunk in water is a no-brainer if it can save lives? Well, it's a no-brainer for me, but for a while there I was criticised as being the vice-president for torture.
"We don't torture. That's not what we're involved in."
Hayden is to appear before the House of Representatives' intelligence committee on Wednesday, also in secret.