McCabe, who served a brief stint as acting director of the bureau after Trump fired ex-FBI chief James Comey, will remain on the payroll until March, when he is eligible to retire with full benefits, NBC said. He had been expected to leave.
Trump and some Republicans in Congress have accused McCabe of political bias, citing his role at the FBI during investigations related to Hillary Clinton and Trump. They question his role in the Clinton email probe and the investigation into Russian efforts to influence the 2016 election and whether the Trump campaign coordinated with the Kremlin.
Trump did not answer when asked by reporters Monday afternoon if he knew about McCabe's move. The White House was not involved in McCabe's decision, press secretary Sarah Huckabee Sanders told reporters Monday afternoon.
"The president was not part of this decision-making process," she said.
She referred questions to the FBI but added that Trump "stands by" his previous comments about McCabe.
The president had thrown jabs at McCabe in a manner unusual for a president and a top FBI official. Trump repeatedly accused McCabe of improper ties to Clinton because former Virginia Gov. Terry McAuliffe — a Clinton ally — backed McCabe's wife's run for a state office in 2015. The Wall Street Journal reported in October 2016 that McAuliffe's political organization gave nearly $500,000 to Jill McCabe's campaign for state Senate.
The FBI says McCabe followed the proper steps to avoid conflicts of interest. His wife's run for office also started months before he had any role in the Clinton probe.
Later Monday, an NBC News report shed more light on the tensions between the president and the Justice Department. A day after Trump fired Comey, he called McCabe to vent and ask why the ex-FBI director got to take a government-funded plane from Los Angeles to Washington.
During the call, Trump suggested that McCabe ask his wife how it feels to be a loser, in an apparent reference to her failed campaign for office, according to NBC.
Other details about Trump's relationship with McCabe surfaced last week, when The Washington Post reported that the president asked him in May who he supported in the presidential election.
In December, the president also tweeted that McCabe was "racing the clock to retire with full benefits."
Former Obama Attorney General Eric Holder praised McCabe's character and blasted "bogus attacks" on federal law enforcement agencies as attempts to distract attention.