The new details about Mr. Kushner’s security clearance, first reported by The Washington Post, emerged hours after Mr. Trump said on Friday that he would leave it up to Mr. Kelly to decide whether Mr. Kushner could continue to hold his interim clearance.

Mr. Trump’s statement set up a potential confrontation between his son-in-law and his chief of staff, who have clashed privately in recent months. In addition to the new policy he announced, which appeared meant to restrict Mr. Kushner’s ability to receive high-level national security information. Mr. Kelly has also tried to restrict Mr. Kushner’s access to the president.

“I will let General Kelly make that decision, and he’s going to do what’s right for the country,” Mr. Trump said at a news conference with Prime Minister Malcolm Turnbull of Australia. “I have no doubt he will make the right decision.”

Pointing to Mr. Kelly, a retired Marine, Mr. Trump said: “General Kelly respects Jared a lot. I will let the general, who’s right here, make that call.” The president praised Mr. Kushner, calling him “truly outstanding” and “an extraordinary dealmaker.”

He noted that Mr. Kushner had been working to broker peace in the Middle East. “The hardest deal to make of any kind is between the Israelis and the Palestinians,” he said. “We’re actually making great headway.”

Mr. Kelly, who has tried to inject discipline and order into Mr. Trump’s freewheeling West Wing, has bristled from the start at Mr. Kushner’s amorphous and omnipresent role, and Mr. Kushner has been angered in turn at what he regards as challenges to his authority and access.

The strains have deepened in recent days, as Mr. Kushner and his wife, Ivanka Trump, have privately disparaged the chief of staff to Mr. Trump, faulting his handling of the scandal surrounding Mr. Porter, the staff secretary who resigned under pressure after spousal abuse allegations became public.

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Mr. Kelly’s memo further inflamed the situation, essentially suggesting that Mr. Kushner might lose the high-level clearance — including to view the presidential daily brief, a summary of intelligence and other sensitive information — that he has enjoyed for more than a year.

At his news conference, Mr. Trump blamed the federal government for the delay on the security clearance, saying there was a “broken system,” and that it took too long for White House employees to have their backgrounds screened by investigators. He complained that it had taken “months and months and months” for some of his staff members to be given their security clearances, despite the fact that some of them do not have complicated financial backgrounds — a factor that sometimes delays background investigations.

While the federal security clearance system has long been criticized as broken and has a backlog of hundreds of thousands of pending applications, senior White House officials almost always have their applications expedited so they can be cleared within weeks and perform their duties.

It is highly unusual for multiple senior officials to spend months serving with only interim clearances, a problem that Mr. Kelly privately began talking about fixing in September.

Mr. Kushner met with Robert S. Mueller III’s investigators briefly last year to discuss his dealings with the former national security adviser, Michael T. Flynn. The interview led Mr. Kushner’s lawyers to believe that he was considered a witness, not a target, in the special counsel investigation.

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