Although US attorneys are political appointees, and the request from Trump's Justice Department is part of a routine process, the move came as a surprise. Not every new administration replaces all US attorneys at once.
A Justice Department spokeswoman confirmed the resignation requests included Bharara, whose office handles some of the most critical business and criminal cases passing through the federal judicial system.
Bharara met with Trump in Trump Tower on Nov. 30. After, Bharara told reporters the two had a "good meeting" and he had agreed to stay on.
On Friday, Bharara was unsure where he stood because he did not know if the person who contacted him about resigning was aware that Trump had asked him to remain in office, according to a source familiar with the matter.
It was not immediately clear if all resignations would ultimately be accepted.
A Justice Department spokesman said on Friday Trump had called Dana Boente, acting US deputy attorney general, to decline his resignation.
Trump also called Maryland US Attorney Rod Rosenstein, his pick to take over as deputy attorney general, to keep him in his post, the spokesman said.
Bharara, appointed by Democratic President Barack Obama in 2009, has pursued an aggressive push against corruption in state and city politics and is known for his prosecution of white-collar criminal cases. He also has been overseeing a federal probe into New York City Mayor Bill de Blasio's fundraising.
In November, he announced charges against two defendants in connection with what he called a multimillion-dollar fraud and kickback scheme at Valeant Pharmaceuticals International Inc.
He has also brought dozens of successful cases against insider traders, including a $1.8 billion settlement and plea deal in 2013 with hedge fund SAC Capital Advisors LP.
His office has secured settlements with companies including General Motors Co and JPMorgan Chase & Co; won several convictions and guilty pleas of former employees of Ponzi scheme operator Bernard Madoff; and prosecuted Suleiman Abu Ghaith, a son-in-law of the late al Qaeda leader Osama bin Laden.
Bharara's priorities have often matched those set by Obama's Justice Department, which potentially puts him at odds with the Trump administration.
Amid an increase in civil rights investigations nationally, for example, Bharara's office joined a lawsuit that led to a settlement in 2015 aimed at reducing violence in New York City's Rikers Island jail complex.
US Senator Chuck Schumer, a Democrat, said in a statement that he was "troubled" to learn of the requests for resignations, "particularly that of Preet Bharara."
As Schumer's chief counsel, Bharara helped lead the investigation of the dismissals of US attorneys in 2006 during the George W. Bush administration.
Robert Capers, US Attorney in Brooklyn, issued a statement saying he had been asked to resign. He said Bridget Rohde, the chief assistant US attorney in that office, would take over his role in an acting capacity.
The Justice Department said on Friday: "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."
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