The dismissal of Mr. Berman came after his office brought a series of highly sensitive cases that worried and angered Mr. Trump and others in his inner circle.
First, there was the arrest and prosecution in 2018 of Michael D. Cohen, Mr. Trump’s longtime legal fixer. Then, there was the indictment last year of a state-owned bank in Turkey with political connections that had drawn the president’s attention. More recently, the Manhattan prosecutors launched an inquiry into Rudolph W. Giuliani, Mr. Trump’s personal lawyer and one of his most ardent supporters.
These simmering tensions finally erupted Friday night in the most public fashion possible as Mr. Barr suddenly announced that Mr. Berman was stepping down — only to discover two hours later that Mr. Berman had made his own announcement: that he was going nowhere.
Given the number of sore spots between Mr. Trump’s Justice Department and its most prominent outpost, it remained unclear precisely what prompted Mr. Barr to seek Mr. Berman’s removal well after nightfall at the start of a summer weekend. At least two of the politically sensitive cases — involving the Turkish bank and Mr. Giuliani — remain ongoing.
Throughout the day on Saturday, many current and former employees of the Southern District of New York, as the Manhattan prosecutors’ office is formally known, marveled at just how sour relations with their colleagues in Washington had gotten. Some worried openly that the move threatened the independence of federal prosecutors.
“While there have always been turf battles between the Southern District and the Justice Department in Washington, and occasionally sharp elbows, to take someone out suddenly while they’re investigating the president’s lawyer, it is just unprecedented in modern times,” said David Massey, a defense attorney, who served as a Southern District prosecutor for nearly a decade.
A spokesman for the office said Mr. Berman would not immediately comment.
The struggle over Mr. Berman came amid a broader purge of administration officials, one that has intensified in the months since the Republican-led Senate acquitted Mr. Trump at an impeachment trial. Since the beginning of the year, the president has fired or forced out inspectors general with independent oversight over executive branch agencies and other key figures from the trial.