She verbally agreed to allow the methods to be used on Abu Zubaydah, an al-Qaeda suspect, in July 2002, a Senate report has revealed.
Miss Rice's role was outlined in a narrative released by the Senate Intelligence Committee as the controversy over alleged torture by the CIA continued to rage.
The information indicates that the programme was approved at the highest levels of the Bush administration.
The new timeline suggests Miss Rice played a more significant role than she acknowledged in written testimony to the Senate Armed Services Committee submitted in the autumn.
It remains unclear, however, who inside the Bush administration first floated the idea of using "waterboarding" – simulated drowning – and other "enhanced" techniques against terrorist suspects in the months after the 9/11 attacks on New York and Washington.
The Senate Intelligence Committee's timeline came a day after the Senate Armed Services Committee released a detailed exhaustive report positing links between the CIA's harsh interrogation programme and abuses of prisoners at the US prison at Guantanamo Bay, Cuba, in Afghanistan and Abu Ghraib prison in Iraq.
Daily revelations about the interrogation programme have followed Mr Obama's decision to release four US Justice Department memos last Thursday.
The memos, running to 126 pages, were written by officials in Mr Bush's Justice Department and contained explicit details of the CIA's methods of extracting information from al-Qaeda suspects between 2002 and 2005.
They revealed that the highly controversial technique of "waterboarding" had been used 266 times on Khalid Sheikh Mohammed and Abu Zubaydah, two senior al-Qaeda prisoners.
After initially indicating he opposed any prosecutions, on Tuesday he said he was open to congressional investigations of Bush administration officials and possible criminal charges.
According to the new timeline, drawn up from legal advice given to the CIA by the Bush administration, Miss Rice personally conveyed the Bush administration's approval for waterboarding of Zubaydah to George Tenet, then CIA Director, in July 2002.
In the autumn, Miss Rice stated to the Senate Armed Services Committee that she had attended meetings where the CIA interrogation request was discussed but could not recall details.
Days after Miss Rice spoke to Mr Tenet, the Justice Department approved the use of waterboarding in a top secret memo. Abu Zubaydah was subjected to waterboarding some 83 times in August 2002.
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