Before they took control of the F.B.I., the bureau’s two top leaders, Kash Patel and Dan Bongino, were some of the agency’s most rabid critics, attacking it at every turn for years.

But now that they are running the agency, the two men have pulled a kind of bait-and-switch: In recent emails to thousands of F.B.I. employees, they have sought to use the bureau’s damaged reputation — a reputation that they themselves helped tear down — as a rationale for bringing reforms to the supposedly broken organization.

“Over the past few years, the F.B.I.’s reputation has been damaged in the eyes of our employers, the American people,” Mr. Patel wrote on Wednesday in one of the messages. “I know each of you, serving across this great nation, are tackling cases that will further the betterment of the communities in which you live and work.”

“Times of change can be uneasy, but they are necessary,” he went on. “Business as usual is no longer business as usual.”

Absent from Mr. Patel’s communications with his 38,000 employees was any mention of the persistent assaults that he himself has launched against the F.B.I. over the years.

Before he ascended to the post of F.B.I. director, Mr. Patel repeatedly distorted the facts about the bureau’s investigation of Russian meddling into President Trump’s 2016 campaign. He has also been a central purveyor of conspiracy theories, accusing federal agents of having helped instigate the attack by Mr. Trump’s supporters on the Capitol on Jan. 6, 2021.