Because he had an interim clearance, Kushner was not supposed to be able to see the president's daily intelligence briefing or have access to other top-secret programme information, one administration official said. But the rules were not enforced with regard to the access rules for the president's son-in-law.
Earlier this month, a top Justice Department official alerted the White House that significant information requiring additional investigation would further delay Kushner's security clearance process, the Washington Post reported last week.
Kushner's inability to obtain a final clearance has frustrated and vexed the White House for months. As someone who meets regularly with foreign officials and reads classified intelligence, he would typically have a fast-tracked background investigation, security clearance experts said.
Friday's downgrade represents a significant loss of access for Kushner, who routinely attended classified briefings, received access to the President's Daily Brief intelligence report and issue requests for information to the intelligence community.
A secret document may be a diplomatic cable from a U.S. embassy to the State Department, discussing the internal politics of that country. The top secret/SCI category, by contrast, includes details of US programmes like drone targeting in Pakistan or covert operations conducted by Special Forces. It also may include high-level private discussions between senior government leaders.
Mark Lowenthal, president of the Intelligence & Security Academy and a former US intelligence official, said Kushner's downgraded clearance level is "a very severe limitation" and should hurt his ability to manage the Middle East peace process.
"This is a very severe limitation because some of the information passing through the White House is more highly classified than 'secret,'" Lowenthal said. "He can no longer see the President's Daily Brief and it also means there are certain meetings he can't be in because most NSC meetings will involve materials above the 'secret' level. The briefings he will get will have to be severely watered down."
Last week, Kelly refused to comment on Kushner's personal status, but did offer a general statement in support of him.
"I will not comment on anybody's specific security clearance situation or go beyond the memo released last week," Kelly said in a statement then. "As I told Jared days ago, I have full confidence in his ability to continue performing his duties in his foreign policy portfolio including overseeing our Israeli-Palestinian peace effort and serving as an integral part of our relationship with Mexico. Everyone in the White House is grateful for these valuable contributions to furthering the President's agenda. There is no truth to any suggestion otherwise."
But Kushner's access immediately appeared threatened when Kelly issued the new policy earlier this month blocking staff with interim clearances from receiving top-secret information. The changes were prompted by intense scrutiny that has followed domestic-abuse allegations against Rob Porter, the president's former staff secretary, who was also working under an interim top-secret clearance.
The move put a "bull's eye" on Kushner, a senior official told The Post.
Kelly had told associates that he was uncomfortable with Kushner's uncertain security clearance status and unique role as both a family member and staffer, according to people familiar with the conversations. He has said he would not be upset if the president's son-in-law and his wife, Ivanka Trump, left their positions as full-time employees.
On Friday, Trump said he would defer the question of Kushner's access to his chief of staff.
"I will let General Kelly make that decision, and he's going to do what's right for the country," the president said during a news conference. "And I have no doubt that he will make the right decision."