Manafort, serving a 7-1/2 year sentence for tax fraud, bank fraud and other charges stemming from Special Counsel Robert Mueller's Russia probe, also faces New York state charges related to residential mortgage fraud, conspiracy and falsifying business records.
The 70-year-old veteran Republican political operative had been expected to be transferred from a federal prison in Pennsylvania to a detention facility in New York ahead of an expected arraignment to face New York charges.
Manafort is being held at the Metropolitan Correctional Center, a federal facility in New York City, the Bureau of Prisons' website showed on Tuesday. Manafort was transferred on Monday, a person familiar with the matter told Reuters.
In a statement, a senior Justice Department official said Manafort's attorneys told the Bureau of Prisons they were concerned about "his health and personal safety" if he was in local custody. New York state prosecutors did not object to the move, which would still make Manafort available to the state when needed, the official said.
"In light of New York's position, and Mr. Manafort's unique health and safety needs, the department determined to err on the side of caution by keeping Mr. Manafort in federal custody during the pendency of his state proceedings," the official said. "This arrangement will not have any impact on his state proceedings."
It was not immediately clear what Manafort's health status was, and an attorney for Manafort did not respond to a request for comment.
Most federal inmates facing charges in New York City are held at the city's scandal-ridden Rikers island jail complex that handles about 9,000 people a day, another city jail known as the Tombs, or Bellevue Hospital, which can accommodate defendants with medical conditions, according to the New York Times.
U.S. Deputy Attorney General Jeffrey Rosen, the Justice Department's new No. 2 under Attorney General William Barr, sent a letter to Manhattan prosecutors telling them he was monitoring Manafort's case, The New York Times reported on Monday.
The U.S. Bureau of Prisons and New York state prosecutors did not immediately respond to a request for comment.
Last week, Manafort's lawyer said he would seek to dismiss the state charges on double jeopardy grounds, which prevent someone from being prosecuted twice for the same act.
Manhattan District Attorney Cyrus Vance's case appears largely tied to some of the same conduct covered in Manafort's federal case, including applications for mortgages secured by properties in New York, but his office could argue an exception is warranted.
Trump has repeatedly praised Manafort, prompting speculation that he could pardon him. However, U.S. presidents can only issue pardons for federal crimes, not state ones.On Monday, the U.S. Supreme Court declined to limit the ability of federal and state prosecutors to separately charge people for the same underlying crime in a ruling that could have implications for Manafort's case.