The F.B.I.’s acting director abruptly retired on Monday as the bureau faces a potentially tumultuous leadership change under the Trump administration.

The move left unclear who would take over once the departure of the acting director, Paul Abbate, took effect at noon. His exit is unusual given that the acting director typically remains in place until a new director is confirmed by the Senate to ensure stability at the highest ranks of the bureau.

Mr. Abbate took command of the bureau on Sunday after Christopher A. Wray, the previous director, announced last month that he would step down before the inauguration. President Trump appointed Mr. Wray in 2017 but publicly attacked him and the F.B.I., which repeatedly investigated him.

In a rare move, Mr. Wray extended the service of Mr. Abbate, who is 57, the mandatory retirement age of certain F.B.I. agents.

In an email to senior F.B.I. officials, Mr. Abbate wrote: “When the director asked me to stay on past my mandatory date for a brief time, I did so to help ensure continuity and the best transition for the F.B.I. Now, with new leadership inbound, after nearly four years in the deputy role, I am departing the F.B.I.”

He added, “I have complete confidence in you and in your ability as a team to continue to carry out our mission of protecting the American people and upholding the Constitution.”

The F.B.I. declined to comment.

Mr. Abbate was named deputy director in February 2021, and Mr. Wray has said it was one of the best decisions he made during his time at the bureau. As deputy, Mr. Abbate oversaw all of the F.B.I.’s domestic and international investigative and intelligence activities and operations. The bureau has about 38,000 employees with agents stationed around the world and other U.S. agencies.

Mr. Trump has said he will nominate Kash Patel, 44, to be the bureau’s next director, but his confirmation hearing has not been scheduled yet.

Mr. Patel worked as a prosecutor at the Justice Department’s national security division from 2014 to 2017 and is expected to face bruising questions about his qualifications. He lacks the experience of previous directors, but his unwavering loyalty to Mr. Trump has catapulted him to consideration for the F.B.I.’s top job.

He has portrayed law enforcement agencies as part of an inept and politicized “deep state,” and he has fiercely criticized the agency and Justice Department over a court-authorized warrant to search for classified documents at Mar-a-Lago, Mr. Trump’s private club and residence in Florida.

In his 2023 book, “Government Gangsters,” Mr. Patel published an extensive enemies list that includes a current F.B.I. agent and an analyst. Mr. Wray also made the list, but Mr. Abbate did not appear on it.

Still, Mr. Patel wrote in his book that the president must “fire the top ranks of the F.B.I.”

Former and current F.B.I. officials are concerned about the drastic changes Mr. Patel has promised at a time that Mr. Wray has said the country faces a serious increase in threats, including from terrorism or from countries like China.

For Mr. Wray, the decision to resign was not an easy one. Last month, he explained to F.B.I. employees why he made the choice, rather than finish out his 10-year term in 2027.

“After weeks of careful thought, I’ve decided the right thing for the bureau is for me to serve until the end of the current administration in January and then step down,” he said. He added that “in my view, this is the best way to avoid dragging the bureau deeper into the fray, while reinforcing the values and principles that are so important to how we do our work.”