President Trump ordered his chief of staff to grant his son-in-law and senior adviser, Jared Kushner, a top-secret security clearance last year, overruling concerns flagged by intelligence officials and the White House’s top lawyer, four people briefed on the matter said.

Mr. Trump’s decision in May so troubled senior administration officials that at least one, the White House chief of staff at the time, John F. Kelly, wrote a contemporaneous internal memo about how he had been “ordered” to give Mr. Kushner the top-secret clearance.

The White House counsel at the time, Donald F. McGahn II, also wrote an internal memo outlining the concerns that had been raised about Mr. Kushner — including by the C.I.A. — and how Mr. McGahn had recommended that he not be given a top-secret clearance.

President Trump repeatedly has denied ever having anything to do with obtaining security clearances for members of his family, including Kushner and Ivanka Trump, who is the First Daughter and White House Advisor to the President.