WASHINGTON — Just hours before he publicly responded last week to the Senate Intelligence Committee report accusing the Central Intelligence Agency of torture and deceit, John O. Brennan, the C.I.A.’s director, stopped by the White House to meet with President Obama.

Ostensibly, he was there for an intelligence briefing. But the messages delivered later that day by the White House and Mr. Brennan were synchronized, even down to similar wording, and the larger import of the well-timed visit was hardly a classified secret: After six years of partnership, the president was standing by the embattled spy chief even as fellow Democrats called for his resignation.

That’s not to say there was no friction between the West Wing and the C.I.A.’s Langley, Va., headquarters after the release of the scorching report. Irritated advisers to Mr. Obama believe Mr. Brennan made a bad situation worse by battling Democrats on the committee over the report during the past year. Some who considered Mr. Brennan the president’s heat shield against the agency when he worked in the White House now worry that since being appointed director, he has “gone native,” as they put it.

But in the 67 years since the C.I.A. was founded, few presidents have had as close a bond with their intelligence chiefs as Mr. Obama has forged with Mr. Brennan. It is a relationship that has shaped the policy and politics of the debate over the nation’s war with terrorist organizations, as well as the agency’s own struggle to balance security and liberty. And the result is a president who denounces torture but not the people accused of inflicting it.