The department described the move as part of an effort to ensure a "uniform transition".
Among those asked to resign included Indian-American Preet Bharara, the US Attorney General for Southern District of New York, who was appointed by Obama in 2009.
Bharara had met Trump in November after his electoral victory. Following the meeting, media reports said that Trump had asked Bharara to stay.
Neither the White House, nor the Department of Justice responded to the questions on Bharara.
In a statement, Flores said that both the George W Bush and Bill Clinton administrations made similar requests at the beginning of their term.
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 Bharara.
"The President initiated a call to me in November and assured me he wanted Bharara to continue to serve as US Attorney for the Southern District," he 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.
"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.
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