News is reporting that the day after FBI Director James Comey was sacked, President Donald Trump called then-acting FBI Director Andrew McCabe to complain that Comey was able to fly home on a government plane.
Mr McCabe has become a target of Republican politicians and the Republican president in connection with the FBI's investigation into Mrs Clinton's use of a private email server while she served as U.S. secretary of state.
McCabe had been widely expected to retire upon his eligibility date, but his departure from the FBI's No. 2 slot is effective Monday, according to the people, who spoke on condition of anonymity to discuss an internal personnel move.
The White House was not involved in McCabe's decision, press secretary Sarah Huckabee Sanders told reporters Monday afternoon.
Trump also reportedly summoned McCabe to his office in May, shortly after he had fired FBI Director James Comey, to ask him whom he voted for in the 2016 elections, The Washington Post reported last week.
The criticism is part of a broader campaign by the president and his supporters alleging that the bureau and special counsel Robert Mueller's Russian Federation investigation are tainted by political bias.
A FBI spokesperson said the bureau had no comment on the reports about McCabe.
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He became deputy director under former FBI Director James Comey, who President Donald Trump fired last May.
"FBI Deputy Director Andrew McCabe is racing the clock to retire with full benefits".
McCabe has also been scrutinized because of politically biased text messages exchanged between Federal Bureau of Investigation counterintelligence official Peter Strzok and Federal Bureau of Investigation attorney Lisa Page.
Trump, who publicly criticized McCabe, allegedly sought to fire McCabe, but the White House never did that because Wray's resignation would have prompted media chaos.
Some exchanges suggest that the two officials had concluded months before the end of the Clinton investigation that the FBI would not charge her with a crime.
With his departure, McCabe joins a list of other top bureau officials who have stepped down in recent days as FBI Director Christopher Wray assembles his own team. In January 2017, the Department of Justice Office of the Inspector General started looking into the handling of the Clinton case, including McCabe's conduct. The president and some congressional Republicans accused him of bias.
Trump was asked on Monday whether he knew McCabe was stepping aside and the president did not answer.
Strzok and Page used words like "idiot" and "loathsome human" to describe Trump during the campaign.