On Tuesday the CIA admitted for the first time it had used waterboarding on three high-profile al-Qaeda suspects, Khalid Sheikh Mohammed, Abu Zubaydah and Abd al-Rahim al Nashiri.
Mohammed has claimed to be the operational mastermind behind the September 11 attacks in the US.
Abu Zubaydah is alleged to have been an aide to Osama bin Laden, the al-Qaeda leader, while al-Nashiri is said to have been the operational commander of the suicide attack on the USS Cole in Yemen in 2000.
Fratto's remarks brought immediate condemnation from the United Nations' special rapporteur on torture, Manfred Nowak, who urged the US to give up its defence of the technique.
"This is absolutely unacceptable under international human rights law," said Nowak.
"Time has come that the government will actually acknowledge that they did something wrong and not continue trying to justify what is unjustifiable."
The admisssion that the CIA had used waterboarding in the past came from the agency's director, Michael Hayden, during testimony to members of the US senate intelligence committee.
Fratto said George Bush, the US president, had authorised Hayden to make the revelations.
He told reporters that if the use of waterboarding was being considered, the CIA boss would approach the attorney general, currently Michael Mukasey, who would then decide whether the practice was legal.
The president would make a final decision on its use, Fratto said.
The US congress is considering banning waterboarding, a move opposed by the Bush administration, which insists it neither uses nor condones torture.
Mukasey told Congress last week that the CIA no longer uses "waterboarding" and that it was not "currently" an authorised interrogation technique.
However, he refused to say whether waterboarding was torture.