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Mr. Brennan, whose nomination is expected to be eventually approved by the Senate, will take charge at the agency where he worked for 25 years just as it faces a sweeping indictment of its now-defunct interrogation program — a blistering, 6,000-page Senate study that includes incendiary accusations that agency officials for years systematically misled the White House, the Justice Department and Congress about the so-called enhanced interrogation techniques like waterboarding that were used on Qaeda prisoners.

By the account of people briefed on the report, it concludes that the program was ill-conceived, sloppily managed and far less useful in obtaining intelligence than its supporters have claimed.

"It's a potential minefield for John Brennan," said Mark M. Lowenthal, a former assistant C.I.A. director and former House Intelligence Committee staff director.

The still-classified report by the Senate Intelligence Committee will place Mr. Brennan squarely in the cross-fire between Democratic critics of what they call a morally and practically disastrous experiment in torture, and some Republican defenders who say the report is biased and fault President Obamafor banning coercive interrogations. And it could place Mr. Brennan in a difficult position inside the agency's headquarters in suburban Virginia.

If he endorses the Senate report, he will be criticizing the many C.I.A. officers who worked on the program and challenging the stance of former directors, notablyGeorge J. Tenet, who oversaw the brutal interrogations, andMichael V. Hayden, who has fervently defended them.

"The career work force will be watching," saidJohn A. Rizzo, a top agency lawyer for 30 years before retiring in 2009. "Hundreds who were part of the seven-year E.I.T. program — and who still believe it was the right and essential thing to do — are still there," he added, referring to enhanced interrogation techniques.

The report, according to statements from some senators and descriptions from others who have reviewed it, documents in exhaustive detail how C.I.A. officials and consultants who ran the program gave top Bush administration officials, members of Congress, the American public and even their own colleagues — possibly including Mr. Brennan himself — a deeply distorted account of its nature and efficacy. After a bipartisan start in 2009, Republican staff members refused to participate in the writing of the report, making the four-year effort largely the work of Democratic committee staff members.

The agency missed a Feb. 15 deadline to complete a review of the report, which has 35,000 footnotes referring to 6 million documents from C.I.A. files. It now appears likely that the response, offering the committee any factual corrections or broader judgments, will be delayed until Mr. Brennan's arrival.

Because Mr. Obama famously said he preferred to look forward, not back at his predecessor's counterterrorism programs, the Senate report is by far the most thorough examination of how the United States came to use nudity, cold, sleep deprivation, stress positions, wall-slamming and waterboarding, methods it had long condemned as abuse or torture.

Mr. Brennan will have to decide whether to support making a redacted version of the interrogation report public, as the committee is likely to support after the C.I.A. completes its review and as a United Nations human rights adviser urged this week. Several Democratic senators and at least one Republican, Senator John McCain of Arizona, who was tortured as a prisoner in North Vietnam, have said that a declassified version must be released, and Mr. Brennan said he would give the request "serious consideration."

He will have to decide whether to convene what the agency calls an accountability board to recommend punishment for current or former officials accused of mismanaging or misrepresenting the interrogation program. If he tries to keep the peace by dismissing the dispute as history and a distraction from the agency's current challenges, he will face strong resistance from the Senate committee's Democratic majority and Mr. McCain.

But Emile A. Nakhleh, a former top C.I.A. analyst on political Islam who once worked for him, said Mr. Brennan's work as Mr. Obama's top counterterrorism adviser, intimate knowledge of the agency and blunt style equip him well to handle the task.

"It will be challenging, but if there's any person who can take this on, it's Brennan," Mr. Nakhleh said. "He may say some harsh things about the program, and some people won't like it. But the institution will benefit."

In the month since Mr. Brennan's public confirmation hearing, the interrogation issue has been largely overshadowed by disputes over the targeted killings of terrorism suspects that Mr. Brennan has overseen from the White House.

On Wednesday, the day after the Senate committee approved Mr. Brennan's nomination in a bipartisan 12-to-3 vote, Senator Rand Paul, Republican of Kentucky, joined by a handful of other senators, carried out a filibuster on the nomination, protesting the Obama administration's refusal to rule out drone strikes on American soil in a national emergency. He ended the filibster Thursday morning, and approval of the nomination is expected soon.

But as the public debate over torture in the movie"Zero Dark Thirty"has shown, the interrogation issue still casts a long shadow over the Central Intelligence Agency nearly a decade after the last waterboarding.

SenatorJohn D. Rockefeller IV, who as the Intelligence Committee's senior Democrat battled to exercise oversight over the interrogation program in its early years, called the new report "the most in-depth and substantive oversight that the committee has undertaken in its entire history" and said it revealed "severe problems at the C.I.A."

Mr. Rockefeller, of West Virginia, said he had spoken with Mr. Brennan at length about the report's findings. "I know that he's as appalled by many of the facts in the report as I am," he said. "John has the expertise, knowledge of the workings of the C.I.A., and the will to make sure that nothing similar ever happens again."

But Mr. Brennan has already been caught between opposing partisan currents. Senator Saxby Chamblissof Georgia, the committee's Republican vice chairman, said at Mr. Brennan's Feb. 7 confirmation hearing that the nominee had told him the report "was not objective" and called it "quote, 'a prosecutor's brief written with an eye toward finding problems.' "

If the C.I.A. pronounces the report "wrong," Mr. Chambliss said, he hoped Mr. Brennan would be willing to stand up for such a conclusion.

For his part, Mr. Brennan said at his hearing that if the report's 350-page executive summary was right, he had himself been misinformed about the program. That would be an extraordinary development, since he was deputy to the agency's third-ranking official in 2002 and 2003, when the program was at its height. He has said that he had no role in running the program and that he expressed disapproval of the brutal methods privately to unidentified colleagues.

"I don't know what the facts are or the truth is. So I really need to look at that carefully and see what C.I.A.'s response is," he said.

"What I'm most interested in, is finding out what went wrong — if this report is, as stated, accurate, what went wrong in the system where there were systemic failures, where there was mismanagement or inaccurate information," Mr. Brennan said. "I would need to get my arms around that, and that would be one of my highest priorities if I were to go to the agency."