The investigation is not related to Trump, the sources added.
Though McEntee traveled alongside Trump, his profile was relatively low compared to other aides with similar tenure, like senior adviser Stephen Miller or the White House's director of social media Dan Scavino.
Even though there are clear security issues with McEntee, that didn't stop him immediately joining the Trump re-election campaign, along with former Trump campaign spokesperson Katrina Pierson.
McEntee declined a CNN request to comment. His abrupt firing came out of nowhere and there was no warning, they said.
Concerns over White House staffers' security clearances have punctuated much of the West Wing news over the past several weeks. He regularly traveled with Trump, and was seen boarding Marine One on the South Lawn of the White House as Trump headed for Pennsylvania on Saturday.
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John McEntee (l.), personal aide to President Trump, was sacked Monday.
He made sure Trump had markers with him while travelling in order to sign autographs, delivered messages to him while at the White House and even set clocks during daylight savings time, according to the Journal.
McEntee joined Trump's campaign in 2015 and remained a strong figure next to the president. That means Kushner, whose portfolio includes the solving the Middle East peace process, no longer has regular access to the nation's most closely guarded secrets as the Federal Bureau of Investigation continues its almost 15-month review of his application for permanent clearance.
As for McEntee, he has not completely left the Trump orbit because he is headed to work for the Trump 2020 campaign.
"We need the help of proven leaders such as Katrina and John to promote the President's growing portfolio of achievements across the country", campaign manager Brad Parscale said in a statement.
The White House has cracked down on staff with temporary security clearances after the scandal around former White House aide Rob Porter.