The full scope of intelligence officials’ concerns about Mr. Kushner is not known. But the clearance had been held up in part over questions from the F.B.I. and the C.I.A. about his foreign and business contacts, including those related to Israel, the United Arab Emirates and Russia, according to multiple people familiar with the events.

During the 2016 presidential campaign, Mr. Kushner was part of a group that met with a Russian lawyer who went to Trump Tower claiming to have political “dirt” on Hillary Clinton. And during the presidential transition, Mr. Kushner had a meeting with the Russian ambassador at the time, Sergey I. Kislyak, and the head of a Russian state-owned bank. When he applied for a security clearance, he did not reveal those meetings.

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.”

During a review of security clearances in February 2018 that was prompted by the controversy surrounding Rob Porter, then the White House staff secretary, 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.