"The Department follows a prescribed process by which an employee may be terminated", Justice Department spokesperson Sarah Isgur Flores said in a statement.
McCabe stepped down from his post as the FBI's second-in-command in January after Trump repeatedly accused him of political bias, but remained on the payrolls in order to qualify for full retirement benefits.
The Justice Department's inspector general concluded that Mr. McCabe was not forthcoming during the review, The Times reported.
An FBI spokeswoman declined to comment.
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The story presented McCabe as a complicated figure - one who lower level officials felt was stymieing their work, even though it detailed McCabe pushing back against Justice Department officials so the case could move forward.
McCabe's retirement is set to go into effect Sunday and his firing could jeopardize his pension as a 21-year veteran of the bureau, according to the report.
Republicans have questioned McCabe's ties to the Democratic Party, considering his wife ran as a Democrat for a Virginia Senate seat in 2015 and got financial help from a group tied to Clinton family ally Terry McAuliffe. President Donald Trump has urged Sessions to fire McCabe so he can't collect.
"Why didn't A.G. Sessions replace Acting FBI Director Andrew McCabe, a Comey friend who was in charge of Clinton investigation", the president demanded to know last June.
The Wall Street Journal story was written by Devlin Barrett, who is now a reporter at The Washington Post. Recently released Federal Bureau of Investigation text messages show that Barrett had talked with the FBI's top spokesman, Michael Kortan, and Federal Bureau of Investigation lawyer Lisa Page, who worked for McCabe, two days before it was published.
A McCabe associate spoke to the Wall Street Journal in October 2016 for an article about a bureaucratic standoff between the FBI and Justice Department over its various investigations into Clinton.