He later made several amendments to that section of his application, known as an SF86. His aides at the time insisted he had omitted those meetings inadvertently.
Mr. Kushner initially operated with a provisional clearance as his background check proceeded.
In an entry to Mr. Kushner’s personnel file on Sept. 15, 2017, the head of the personnel security division, Carl Kline, wrote, “Per conversation with WH Counsel the clearance was changed to interim Top Secret until we can confirm that the DOJ or someone else actually granted a final clearance. This action is out of an abundance of caution because the background investigation has not been completed.”
In a statement to The Times when Mr. Kushner received the clearance last year, Mr. Lowell said that “his application was properly submitted, reviewed by numerous career officials and underwent the normal process,” Mr. Lowell said.
During a review of security clearances in February 2018 that was prompted by the controversy surrounding the then-White House staff secretary, Rob Porter, who had been accused of domestic abuse, Mr. Kushner’s clearance was downgraded from interim top secret to secret, limiting his access to classified information. At the time, Mr. Kelly wrote a five-page memo, revoking temporary clearances that had been in place since June 1, 2017.
That affected both Mr. Kushner and Ms. Trump, who told friends and advisers that they believed that Mr. Kelly and Mr. McGahn were targeting them for petty reasons instead of legitimate concerns flagged by officials.
Both complained to the president about the situation, current and former administration officials said. In Mr. Kushner’s case, Mr. Trump would often turn to other aides and say in frustration, “Why isn’t this getting done?” according to a former administration official. On at least one occasion, the president asked another senior official if the person could sort out the issue. That official said no, according to this account.
Mr. Kelly did not believe it was appropriate to overrule the security clearance process and had brushed aside or avoided dealing with Mr. Kushner’s requests, a former administration official said. Mr. Kelly did not respond to a request for comment.