That apparently came as news to Geoffrey Berman.
Mr Berman oversaw the prosecution of a number of Mr Trump's associates.
Attorney General Bill Barr said on Saturday that Trump ordered the removal of Geoffrey S. Berman, United States attorney for the Southern District of NY, after he had refused to step down on Friday night.
Mr Berman insisted he would stay in post and continue his investigations.
"I have not resigned, and have no intention of resigning", Berman wrote.
The standoff marks the latest in series of unusual actions by Attorney General William Barr that critics say are meant to benefit Mr Trump politically and undermine the independence of the Justice Department.
Berman's team aggressively investigated and prosecuted Trump's former personal attorney and fixer, Michael Cohen.
"This late Friday night dismissal reeks of potential corruption of the legal process", he said in a statement. The White House quickly announced that Trump was nominating the chairman of the Securities and Exchange Commission to the job, a lawyer with virtually no experience as a federal prosecutor.
Attorney General Bill Barr's effort to push out one of the most powerful prosecutors in the country ran into headwinds Saturday, with Republicans signaling little appetite to fight to confirm a new United States attorney amid Democratic accusations that the move was an effort to shield President Donald Trump's associates from federal investigation. What is angering President Trump? At the time, Berman had already been installed in NY office.
"I learned in a press release from the Attorney-General tonight that I was "stepping down" as United States Attorney", Geoffrey Berman said in a statement.
He oversaw the prosecution of Michael Cohen, Mr Trump's former personal lawyer, indicted two Giuliani associates and launched a probe into Mr Guiliani in connection with his efforts to dig up dirt in the Ukraine on Mr Trump's political adversaries.
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A Justice Department official, asked about Berman's refusal to leave the post until a successor is confirmed, told Reuters the "timeline remains the same" as Barr had laid out in announcing the replacement.
President Trump has yet to weigh in publicly on Berman's firing.
It also comes as Trump seeks to purge officials perceived as not fully supporting him.
Craig Carpenito, now the United States Attorney for the District of New Jersey, will serve as the Acting United States Attorney for the Souther District of NY starting July 3rd as the Senate considers Clayton's nomination.
The outlet quoted sources in the Justice Department as saying Berman had been offered other positions at the office, including the head of the civil division.
A senior department official said Clayton was planning to leave the administration, wanted to move back to NY and expressed interest in the Southern District position, and Barr thought he would be a good fit, said the official, who was not authorized to publicly discuss internal department matters and spoke on condition of anonymity.
But the Justice Department's Office of Legal Counsel argued in a 1979 opinion that the "power to remove a court-appointed US attorney rests with the president". Collins, who represented western NY, has since resigned.
In the House, Representative Gerry Connolly of Virginia, a member of the Oversight Committee, said the Justice Department owes the Congress an explanation for this "constitutional crisis".
The Trump administration has fired several officials tasked with government oversight.
Pending Clayton's Senate confirmation, Trump has appointed Craig Carpenito, now the U.S. Attorney for the District of New Jersey, to be the Acting United States Attorney for the Southern District of NY, added Barr. Deviation from that norm, especially under the particular circumstances at work here, is more than a little troubling.
Yet the links between the White House and some of Berman's investigations were clear. They pretty clearly serve at the pleasure of the President, regardless of whether they were directly or indirectly appointed.