The federal inquiry into Kushner's background has been ongoing since previous year. It also provided another layer of intrigue to the acrimonious relationship between Kushner and Kelly, who have been at odds over access to the President and the classified materials he views.
Trump's son-in-law, Jared Kushner, is one of the president's top advisers and works on a myriad of high-level and sensitive national security issues such as brokering peace in the Middle East.
Kelly a week ago set Friday as the deadline for adjudicating the cases of Kushner and others in clearance limbo.
That isn't sitting well with chief of staff John Kelly, who warned he would crack down today.
Kushner's attorney has acknowledged that Kushner's security clearance application has yet to be approved and said "my inquiries to those involved again have confirmed that there are a dozen or more people at Mr. Kushner's level whose process is delayed". But several former officials from Republican and Democratic administrations have raised concerns over his ability to do his job without top secret clearance. The phone call was first reported by The Washington Post. That episode also prompted Kelly's crackdown on interim clearances.
The source said there were frustrations on both sides between Kushner and Kelly and they wanted to find a solution.
CNN reported Thursday that Kushner's clearance to see top secret information on a long-term basis is being held up by Robert Mueller's Russian Federation probe. But the President's advisers have determined that taking that step would be drastic and cause deep rifts within the intelligence community and among Trump's top aides.
In a statement last week, Kelly said that Kushner would have access to information important to his diplomatic information, but declined to say whether he would get full clearance.
"That will be up to General Kelly".
"Gen. Kelly respects Jared a lot", Trump said. What I've heard in recent days this could be a place where John Kelly goes, and Trump doesn't appoint a chief of staff. "I have no doubt he will make the right decision". This issue would continue in the event that Kelly were forced out.
"We inherited a system that's broken. There is no truth to any suggestion otherwise", he said.
In addition, Kushner's actions during the transition have been noted in the guilty plea of former Trump national security adviser Michael Flynn, who admitted he lied to the Federal Bureau of Investigation about contacts with then-Russian Ambassador Sergey Kislyak.
Kushner is reportedly said to review the highly secret presidential daily brief each morning and has been in the room for some of Trump's most consequential domestic and foreign policy decisions. "He works for nothing".