While the Senate considers Mr Clayton's nomination, Mr Trump has appointed Craig Carpenito, the US Attorney for the District of New Jersey, as the acting US Attorney for the Southern District of New York, Mr Barr said in his statement.
Giuliani's associates - who also have ties directly to Trump - Lev Parnas and Igor Fruman are now under indictment from the office.
On Friday evening, Attorney General Bill Barr announced that US Attorney Geoffrey Berman, the powerful federal prosecutor from the Southern District of NY who's investigated multiple Trump associates, was "stepping down", with President Trump intending to nominate SEC Chair Jay Clayton to Berman's role, even though Clayton has no prosecutorial experience.
A Justice Department official, asked about Mr Berman's refusal to leave the post until a successor is confirmed, said the "timeline remains the same" as Mr Barr laid out in announcing the replacement. "I have not resigned, and have no intention of resigning, my position, to which I was appointed by the Judges of the United States District Court for the Southern District of NY".
His statement came hours after Attorney General William Barr said Berman was stepping down from his position.
The standoff set off an extraordinary clash between the Justice Department and one of the nation's top districts, which has tried major mob and terror cases over the years. Ukraine-born ally of Rudy Giuliani was accused by USA prosecutors of skirting campaign contribution limits as part of a scheme to oust the American ambassador to Ukraine, an episode now under scrutiny by a Congressional committee weighing the impeachment of President Donald Trump.
Companies recognizing Juneteenth on Friday
But she made a decision to give her 16 employees the day off when she saw big tech companies doing it, and after New York Gov. We actually sent a link around to the Juneteenth episode to everyone at ABC Entertainment in advance of Friday's holiday".
Berman's team aggressively investigated and prosecuted Trump's former personal attorney and fixer, Michael Cohen. The White House never said why Trump didn't formally nominate Berman.
He added that he would only step down when a presidentially appointed nominee was confirmed by the Senate. The judges were legally obligated to fill the position because Trump left it vacant without a Senate-confirmed attorney for more than one year.
To say this is rather unusual would be to understate matters considerably. He has taken a direct hand in other investigations that have angered Trump. "I have not resigned, and have no intention of resigning my position, to which I was appointed by the Judges of the United States District Court for the Southern District of New York" (SDNY), Berman said in a statement. He has been the U.S. attorney for Manhattan since 2018, and under his leadership, his office prosecuted Trump's former attorney Michael Cohen, is investigating top Trump confidante Rudy Giuliani and indicted the former NY mayor's associates Lev Parnas and Igor Fruman. But the various investigations are still ongoing and no charges seem imminent, said the people familiar with the matter, who weren't authorized to publicly discuss the matter and spoke to The Associated Press on condition of anonymity.
He also led the investigation into Jeffrey Epstein and earlier this month accused Prince Andrew of "shutting the door" on his probe.
It also comes as Trump seeks to purge officials perceived as not fully supporting him. He has fired or forced out inspectors general with independent oversight over executive branch agencies and other key figures from the trial.
Barr said in his letter that the deputy US attorney, Audrey Strauss, would take over the top job until a permanent successor is in place.
'Huge Victory for LGBTQ Equality' as US Supreme Court Affirms Workplace Protections
Alphonso David, the group's president, said , "No one should be denied a job or fired simply because of who they are or whom they love".
House Judiciary Committee Chairman Jerry Nadler tweeted, "America is right to expect the worst of Bill Barr, who has repeatedly interfered in criminal investigations on Trump's behalf". Collins 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".
Preet Bharara, who preceded Berman in the office was sacked in the early days of the Trump administration tweeted, "Doesn't sound like 'stepping down'".
The U.S. Attorney for the Southern District of NY is in a fight with the Justice Department over his job.
That this is further politicization of the Justice Department goes without saying. Deviation from that norm, especially under the particular circumstances at work here, is more than a little troubling. Because of this, it was not immediately clear whether Barr could force Berman out.
Kenya defeats Djibouti to win a seat at the UN Security Council
Each new Security Council member needs to win two-thirds of the votes cast - meaning 128 votes if all 193 nations vote. The combo photo shows the national flags of India (Up Left), Ireland (Up Right), Mexico (Down Left) and Norway.