The top agent at the F.B.I.’s New York field office said in an email Monday that he had been forced out of his job, following clashes with Justice Department officials over Trump administration directives.

The veteran agent, James E. Dennehy, was told Friday to retire from his role leading the F.B.I.’s largest field office, delivering another blow to the senior ranks of the bureau. Mr. Dennehy, who had been running the office since September, had angered Trump administration officials by supporting bureau leaders who resisted turning over the names of those who investigated the Jan. 6, 2021, attack on the U.S. Capitol.

Mr. Dennehy had also angered Attorney General Pam Bondi by what she claimed was the New York office’s failure to turn over all the investigative files related to Jeffrey Epstein, the financier charged with sex trafficking who killed himself in prison. Ms. Bondi provided no evidence to back up her assertion.

“Late Friday, I was informed that I needed to put my retirement papers in today, which I just did,” Mr. Dennehy wrote Monday in an email to colleagues. “I was not given a reason for this decision. Regardless, I apologize to all of you for not being able to fulfill my commitment to you.”

Mr. Dennehy’s departure comes after weeks of turmoil at the F.B.I. that saw nearly a dozen executives at headquarters removed unexpectedly, leaving a leadership vacuum and confusion on the seventh floor of the Hoover Building in Washington, D.C.

It is not clear what role Kash Patel, the new director of the F.B.I., played in Mr. Dennehy’s ouster. But on Friday — the same day that Mr. Dennehy was told to leave — Mr. Patel produced a two-minute video that was sent to bureau employees. In it, he pledged support for his subordinates.

“I will fight for you every single day,” he said. “I will take all the criticism.”

The forced departure of Mr. Dennehy, a respected leader, is sure to further rattle an organization already under siege.

Mr. Dennehy, who served for seven years as a U.S. Marine officer before joining the bureau in 2002, spent most of his career investigating or supervising counterintelligence cases, which, in essence, involved chasing spies rather than building criminal cases.

Before being named to head the agency’s flagship office in New York, he headed its office in Newark for two years. But he spent the bulk of his career in New York and at headquarters in Washington, including leading New York’s counterintelligence and cyber division.

On Friday, Ms. Bondi said without offering corroboration that Mr. Dennehy’s office had deliberately held back information sought by Justice Department headquarters.

She wrote in a letter Thursday to Mr. Patel that she had been “repeatedly assured by the F.B.I.” that she had been given a full set of documents related to the investigation and indictment of Mr. Epstein.

Her letter, however, suggested the F.B.I. office in New York had turned over only a small fraction of that paperwork.

“When you and I spoke yesterday, you were just as surprised as I was to learn this new information,” her letter to Mr. Patel said. The letter imposed a deadline of last Friday morning for the F.B.I. to “deliver the full and complete Epstein files to my office.” She also ordered “an immediate investigation into why my order to the F.B.I. was not followed.” Later that day, Mr. Dennehy was told to resign.

In January, the acting leaders of the F.B.I., Brian Driscoll and Robert Kissane, refused to provide a list of personnel involved in the Jan. 6 cases. Emil Bove, the acting No. 2 in the Justice Department, accused the men of being insubordinate. Ultimately, the F.B.I. turned over the information.

In a defiant and eloquent email at the time, Mr. Dennehy came to their defense and urged his staff to “dig in” after the Trump administration targeted officials involved in the investigations into the Jan. 6 attack. He also praised the bureau’s interim leaders for defending its independence.

On Monday, he wrote that among the top qualities he would miss about the bureau was that independence.

“We will not bend. We will not falter. We will not sacrifice what is right for anything or anyone,” he wrote.

In the email, he used pointed language that echoed his earlier message to the rank and file.

“I’ve been told many times in my life, ‘When you find yourself in a hole, sometimes it’s best to quit digging.’ Screw that. I will never stop defending this joint. I’ll just do it willingly and proudly from outside the wire,” Mr. Dennehy wrote.