Those records, the sources said, show that Brennan was a regular recipient of CIA message traffic about controversial aspects of the agency's counter-terrorism program after September 2001, including the use of "waterboarding."
How deeply involved Brennan was in the program, and whether he vigorously objected to it at the time, as he has said he did, are likely to be central questions lawmakers raise at his Senate Intelligence Committee confirmation hearing, scheduled for February 7.
After Brennan temporarily left government service in 2005, he publicly disavowed waterboarding, a form of simulated drowning, and other physically painful techniques that are often described as torture.
The official records, which include raw CIA operational message traffic that remains classified, are silent on whether he opposed the techniques while at the spy agency, said the sources, who spoke on condition of anonymity. Brennan served as deputy executive director of the agency beginning in 2001.
Some former officials familiar with deliberations about the program said they don't recall Brennan voicing objections to the use of harsh interrogation techniques.
But other former officials say Brennan was among agency officials who were uncomfortable with the use of physically coercive tactics, despite the legal opinions that supported their use. He expressed concern, according to these officials, that if details of the program became public, it would be CIA officers who would face criticism, rather than the politicians and lawyers who approved them.
"If John says he expressed reservations about some techniques, I believe him because he's an honest guy," said John McLaughlin, who was deputy CIA director at the time.
"Mr. Brennan had significant concerns and personal objections to many elements of the EIT (enhanced interrogation techniques) program while it was under way," a senior administration official said in response to Reuters' inquiries. "He voiced those objections privately with colleagues at the agency."
The question of whether and to what extent Brennan raised objections will be a focus of his confirmation hearing for Republican and Democratic senators alike.
"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 programs while serving at the CIA during the last administration," Senator John McCain, who was tortured during captivity in North Vietnam, said recently.
KNOWLEDGE, BUT NOT RESPONSIBILITY
Under the CIA program, which largely ended before Obama took office, captured militants were detained and interrogated in a network of secret CIA prisons. Sometimes, they were delivered to foreign governments through an extralegal process called "extraordinary rendition."
Three high-ranking al Qaeda leaders, including Khalid Sheikh Mohammed, the alleged mastermind of the September 11 attacks on the United States in 2001, were waterboarded.
Because he was a regular recipient of operational traffic related to the interrogation and detention program, Brennan's name appears in a secret draft of a 6,000-page Senate Intelligence Committee investigative report on the program, sources familiar with that report said. They added, however, that he was cited in passing, not as a significant supervisor or manager of the program.
Brennan, who is now Obama's White House counter-terrorism adviser, played no role in the program's "creation, execution or oversight," the senior Obama administration official said.
"(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."
SECOND TRY FOR CIA
This is the second time that Obama has sought to nominate Brennan to head the spy agency, and the second time that questions have arisen about his involvement in enhanced interrogation tactics when he was a CIA official during the administration of former President George W. Bush.
Brennan's candidacy for the top CIA job was derailed over the issue when he was an early front-runner for it after Obama's 2008 election victory.
Brennan withdrew his name from consideration at that time and, in a letter to President-elect Obama, said he had been a "strong opponent" of Bush-era policies, including the Iraq war and coercive interrogation techniques.
Brennan instead became Obama's White House counter-terrorism adviser. Obama issued an executive order banning the techniques shortly after taking office.
Barring unexpected revelations, most political handicappers believe Brennan will be confirmed as CIA director this time.