A prominent US prosecutor says the Trump administration fired him after he refused to quit, adding a discordant note to what is normally a routine changing of top attorneys when a new president takes office.

New York US Attorney Preet Bharara's defiant exit, first announced on Twitter has raised questions about President Donald Trump's ability to fill top jobs throughout his government.

Trump has yet to put forward any candidates to serve as the nation's 93 district attorneys even as his Justice Department asked the 46 who have not yet quit to hand in their resignations on Friday. Key positions at agencies like the State Department and the Defense Department also remain unfilled.

As the federal prosecutor for Manhattan and surrounding areas since 2009, Bharara secured insider-trading settlements from Wall Street firms and won criminal convictions in high-profile corruption and terrorism cases.

He told reporters in November that Trump had asked him to stay in his post, and he refused to resign when asked to do so by the Justice Department on Friday. He said he was fired on Saturday afternoon.

"Serving my country as US Attorney here for the past seven years will forever be the greatest honour of my professional life, no matter what else I do or how long I live," Bharara said in a press statement.

Like all US attorneys, Bharara is a political appointee who can be replaced when a new president takes office. Previous presidents have often asked outgoing US attorneys to stay on the job until their replacements win confirmation in the US Senate.

The Washington Post, citing two people close to Trump, said the president's adviser Stephen Bannon and Attorney General Jeff Sessions wanted a clean slate of federal prosecutors to assert the administration's power.

But the decision to replace so many sitting attorneys at once has raised questions about whether the Trump administration's ability to enforce the nation's laws would be hindered.