In all there are 93 US attorneys. Many of them have already left their positions, but 46 attorneys who stayed on in the first weeks of the Trump administration have been asked by US Attorney General Jeff Sessions to resign "in order to ensure a uniform transition," Justice Department spokeswoman Sarah Isgur Flores said on Friday.
Defending the move, Flores in a statement said that both the George W Bush and Bill Clinton administrations made similar requests at the beginning of their term.
Among those asked to resign included Mr Bharara, the US Attorney General for Southern District of New York, who was appointed by Obama in 2009.
Mr Bharara, who has earned the reputation of a "crusader" prosecutor, had met President Trump in November after his electoral victory.
Following the meeting, media reports said that President Trump had asked Mr Bharara to stay.
Neither the White House, nor the Department of Justice responded to the questions on Mr Bharara.
48-year-old Mr Bharara has made a national and international mark for himself with many high-profile cases and investigations including foreign countries, insider trading and those involving US politicians. It was under his prosecution that India-born former Goldman Sachs director Rajat Gupta was convicted for insider trading in 2012.
New York Senator Charles Schumer said he is "troubled" to learn the reports of requests for resignations from the remaining US Attorneys, particularly that of Mr Bharara.
"The President initiated a call to me in November and assured me he wanted Mr Bharara to continue to serve as US Attorney for the Southern District," he said.
"By asking for the immediate resignation of every remaining US Attorney before their replacements have been confirmed or even nominated, the President is interrupting ongoing cases and investigations and hindering the administration of justice," Mr Schumer said.
"Until the new US Attorneys are confirmed, the dedicated career prosecutors in our US Attorney's Offices will continue the great work of the Department in investigating, prosecuting and deterring the most violent offenders," the Justice Department said.
Senator Dianne Feinstein, Ranking Member of the Senate Judiciary Committee Dianne Feinstein, said she is surprised to hear that Trump and Sessions have abruptly fired all 46 remaining US attorneys.
"At a time when Attorney General Sessions has recused himself from major investigations into the Trump campaign, the independence of federal prosecutors could not be more important. That's why many of us have called for the appointment of a special prosecutor," she said.
"Under previous administrations, orderly transitions allowed US attorneys to leave gradually as their replacements were chosen. This was done to protect the independence of our prosecutors and avoid disrupting ongoing federal cases," Feinstein said.