Attorney General William P. Barr on Friday night abruptly tried to fire the top federal prosecutor in Manhattan, Geoffrey S. Berman, who has investigated several of President Trump’s closest associates, but Mr. Berman said he would not leave.

The clash focused new attention on the efforts by Mr. Trump and his closest aides to rid the administration of officials whom the president views as insufficiently loyal. It also touched off a crisis within the Justice Department over one of its most prestigious jobs, at a time when the agency has already been roiled by questions over whether Mr. Barr has undercut its tradition of independence from political interference.

Mr. Berman, the United States attorney for the Southern District of New York, and his team have been at the forefront of corruption inquiries in Mr. Trump’s inner circle. They successfully prosecuted the president’s former personal lawyer, Michael Cohen, who went to prison, and have been investigating Mr. Trump’s current personal lawyer, Rudolph W. Giuliani.

“I have not resigned, and have no intention of resigning, my position,” Mr. Berman said in a statement, adding that he learned that he was “stepping down” in a press release from the Justice Department.

Mr. Barr’s announcement that President Trump was seeking to replace Mr. Berman was made with no notice. Mr. Barr said the president intended to nominate as Mr. Berman’s successor Jay Clayton, the chairman of the Securities and Exchange Commission, who has never served as a prosecutor.

Mr. Barr asked Mr. Berman to resign but he refused so Mr. Barr moved to fire him, according to a person familiar with the matter. Mr. Trump had been discussing removing Mr. Berman for some time with a small group of advisers, the person said. Mr. Trump has been upset with Mr. Berman ever since the Manhattan prosecutor’s office pursued a case against Mr. Cohen.

Mr. Trump’s purge of officials has intensified in the months since the Republican-led Senate acquitted him in the impeachment trial. He has fired or forced out inspectors general with independent oversight over executive branch agencies and other key figures from the trial.

Several dismissals have come late on Friday nights, a time that many White Houses have used to disclose news that they would prefer receive little attention.

The highly public tussle between Mr. Barr and Mr. Berman that unfolded late on Friday was another example of the tumult that has engulfed the Justice Department in recent months.

The attorney general’s interventions in high-profile cases involving the onetime Trump advisers Roger J. Stone Jr. and Michael T. Flynn have prompted accusations from current and former law enforcement officials that Mr. Barr has politicized the department.

Mr. Berman’s office has taken an aggressive approach in a number of cases that have vexed the Trump administration, from the prosecution and guilty plea obtained from Mr. Cohen to a broader investigation, growing out of that inquiry, which focused on Mr. Trump’s private company and others close to him.

Over the last year, Mr. Berman’s office brought indictments against two close associates of the president’s current lawyer, Mr. Giuliani, and began an investigation into Mr. Giuliani himself, focusing on whether his efforts to dig up dirt in Ukraine on the president’s political rivals violated laws on lobbying for foreign entities.

Mr. Berman’s office also conducted an investigation into Mr. Trump’s inaugural committee, subpoenaing financial and other records as part of a broad inquiry into possible illegal contributions from foreigners.

A lawyer for Mr. Giuliani, Robert J. Costello, said he had no advanced notice of Mr. Barr’s effort to oust Mr. Berman. Mr. Costello said Mr. Giuliani had no role in the matter.

“We certainly don’t know anything about it,” Mr. Costello said. “This comes as a surprise to us.”

Mr. Berman’s abrupt removal came just days after Mr. Trump’s former national security adviser, John Bolton, alleged in his new book that Mr. Trump sought to interfere in an investigation by Mr. Berman’s office into a Turkish bank, in a bid to cut deals with the Turkish president, Recep Tayyip Erdoğan.

The United States attorney’s office in Manhattan is perhaps the most famous federal prosecutor’s post in the country. The office, through Democratic and Republican administrations, has long prized a tradition of independence from the Justice Department and Washington, and was even nicknamed the “Sovereign District of New York.”

Mr. Berman worked there in the 1990s as prosecutor, but he took over the office under unusual circumstances.

A Republican who contributed to the president’s campaign and worked at the same law firm as Mr. Giuliani, Mr. Berman was never formally nominated for the position by President Trump or confirmed by the Senate, as is normal protocol for United States attorneys.

In 2018, the attorney general at the time, Jeff Sessions, appointed Mr. Berman as interim United States attorney in Manhattan.

But President Trump never formally sent Mr. Berman’s nomination to the Senate. After 120 days, his formal appointment to the post was made by the judges of the United States District Court.

Mr. Berman took note of the nature of his appointment to the position in explaining why he was refusing to step down.

“I was appointed by the judges of the United States District Court for the Southern District of New York,” Mr. Berman said in his statement. “I will step down when a presidentially appointed nominee is confirmed by the Senate. Until then, our investigations will move forward without delay or interruption.”

U.S. attorneys are typically replaced by their first assistants, but Mr. Berman is being replaced by an outsider who has never worked in that office.

Mr. Clayton is not a litigator or a former prosecutor, which often are prerequisites to being named a United States attorney, especially to a post like the one running the Southern District.

Before being named chairman of the Securities and Exchange Commission by President Trump, Mr. Clayton had been a longtime corporate lawyer at Sullivan & Cromwell, where he did work for banks, hedge funds and big corporations such as Goldman Sachs, Barclays and Alibaba.

It is a highly unusual to name an outsider to a prosecutor’s post like the one in Manhattan, but it is not the first time this has happened under Mr. Trump. When Jessie K. Liu left the United States Attorney’s office in Washington, she was replaced by an ally of Mr. Barr, Timothy Shea, rather than her first assistant.

Mr. Barr met with Mr. Berman on Friday in New York, according to a person familiar with the matter. It was not clear what they discussed.

Mr. Barr was visiting New York to meet with senior New York Police Department officials and to talk about “policing issues that have been at the forefront of national conversation and debate,” according to a Justice Department press release.

On Thursday, Mr. Berman sent a message to the office about safety protocols for returning to work, sounding upbeat and giving no indication he was about to leave, according to a person familiar with the message.

Mr. Berman’s departure came two days after excerpts released from the upcoming book of Mr. Bolton showed what Mr. Bolton said was Mr. Trump’s willingness to intervene in criminal investigations, including one in Mr. Berman’s office.

Mr. Bolton wrote in the book that Mr. Trump in 2018 had promised the Turkish president, Mr. Erdogan, that he would interfere in an ongoing investigation against a Turkish company accused of violating Iranian sanctions.

“Trump then told Erdogan he would take care of things, explaining that the Southern District prosecutors were not his people, but were Obama people, a problem that would be fixed when they were replaced by his people,” Mr. Bolton wrote, according to an excerpt published this week in The Washington Post.

At the time, Mr. Berman was the U.S. attorney overseeing the case. The company, Halkbank, a state-owned bank in Turkey, was indicted in the Southern District last year.

Mr. Berman was also known for his office’s decision last year to bring sex-trafficking charges against Jeffrey Epstein, who had avoided a similar prosecution in Florida in 20008.

After Mr. Epstein committed suicide last August, Mr. Berman announced that the inquiry into Mr. Epstein’s sex trafficking conspiracy would continue and that his office was committed to standing up for the “brave young women” whom Mr. Epstein had abused.

The office has been investigating several of Mr. Epstein’s co-conspirators, and has been locked in a public dispute with Prince Andrew of Britain about what Mr. Berman has depicted as the prince’s refusal to assist the investigation.

Matthew Goldstein contributed reporting.