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…

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, notably George J. Tenet, who oversaw the brutal interrogations, and Michael V. Hayden, who has fervently defended them.

“The career work force will be watching,” said John 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.