The man expected to be the next CIA chief had detailed knowledge of "enhanced interrogation techniques" including waterboarding, sources claim.
John Brennan, who is likely to be confirmed before the Senate Intelligence Committee on February 7, publicly disowned waterboarding and other painful techniques when he temporarily left government service eight years ago.
But unnamed sources told Reuters that Brennan was fully aware of the most controversial aspects of the agency's counter-terrorism programme, including techniques akin to torture, during his time as its deputy executive director between 2001 and 2005.
Other officials claimed they don't recall Brennan objecting to the use of extreme interrogation techniques. But John McLaughlin, deputy CIA director at the time, said Brennan was "uncomfortable" with those techniques.
"If John says he expressed reservations about some techniques, I believe him because he's an honest guy," McLaughlin said.
However, Republican senator John McCain has promised he will grill Brennan at the confirmation hearing.
"I have many questions and concerns about his nomination to be director of the Central Intelligence Agency, especially what role he played in the so-called enhanced interrogation programmes while serving at the CIA during the last administration," he said.
McCain is a veteran of the Vietnam war and was tortured during captivity.
Among three top level al-Qaida leaders who were definitely waterboarded under the CIA programme, exposed during the reign of former President George Bush, is Khalid Sheikh Mohammed, the alleged mastermind of the 9/11 attacks.
Brennan's name appeared in a secret draft of a 6,000-page Senate intelligence committee investigative report on the CIA programme, sources said, but only as someone "informed about the facts".
Apparently he played no role in the program's creation, execution or oversight, according to a senior Obama administration official.
"(Brennan) was on hundreds if not thousands of messages a day regarding many different issues but his primary responsibility was ... helping manage the day-to-day running of the agency, to include support, logistics, IT, budget, personnel resources, facilities, IG (Inspector General) recommendations, and the like," he said.
Brennan was initially made a candidate for the top CIA job by Obama in 2008, but he pulled out of the running after allegations that he was implicated in the CIA programme under investigation.