Trump has previously complained about how Manafort was being treated and has suggested he might pardon him.
Manafort, 70, who is currently serving out a federal prison sentence in Pennsylvania, was expected to be transferred to the infamous Rikers complex as he waited to face mortgage fraud and other state charges brought by the Manhattan District Attorney's office.
But in a statement to ABC News Monday evening, a senior DOJ official acknowledged that the department stepped in to the dispute last week after Manafort's attorneys raised concerns "related to his health and personal safety." During his federal trial, Manafort's physical condition appeared to be deteriorating and at times during hearings he had to use to a wheelchair or a cane.
The New York Times reported Monday that among the DOJ officials to get directly involved was Deputy Attorney General Jeffrey Rosen, who was confirmed to his position as the department's number 2-ranked official last month.
"Mr. Manafort’s attorneys proposed that he remain in federal custody and be made available to the state when necessary," the official said. "The Department requested the views of New York prosecutors, who did not object to Mr. Manafort’s proposal. In light of New York’s position, and Mr. Manafort’s unique health and safety needs, the Department decided to err on the side of caution by keeping Mr. Manafort in federal custody during the pendency of his state proceedings."
Manafort has since been transferred to the Metropolitan Correctional Center in Lower Manhattan ahead of his expected arraignment on the state charges.
His attorneys did not immediately respond to a request for comment from ABC News.
Several former Obama-era federal prosecutors raised issue with the high-level DOJ intervention, noting it ran counter to typical rules governing detention for federal inmates facing state charges in New York.
President Trump has repeatedly expressed his objections to the treatment of Manafort by federal prosecutors in special counsel Robert Mueller's Russia investigation.
After the Manhattan District Attorney announced separate state charges against Manafort in March of this year, Trump reacted telling reporters, "on a human basis, it's a very sad thing."
The White House did not immediately respond to ABC News' request for comment on the DOJ decision.
ABC's Katherine Faulders and Aaron Katersky contributed to this report.