In a statement released Friday, Abbe D. Lowell, Mr. Kushner’s lawyer, declined to say whether his client would still have a security clearance, saying only that “the new policy announced by Mr. Kelly will not affect Mr. Kushner’s ability to continue to do the very important work he has been assigned by the president.”
It was unclear Friday night how Mr. Kushner could do his job without a security clearance, though Mr. Trump, as president, might be able to overrule Mr. Kelly’s process and grant Mr. Kushner the access that he needs. It is also possible that Mr. Kushner’s background review did not begin until after June 1, which could allow him to retain a temporary clearance.
Mr. Kelly’s memo, which was released publicly after Mr. Trump left Washington for a weekend in Palm Beach, Fla., acknowledges that mistakes and shortcomings were exposed by the handling of marital abuse allegations against one of President Trump’s top aides.
“We should — and, in the future, must — do better,” Mr. Kelly wrote in a document addressed to senior White House officials and copied to the directors of the country’s intelligence and law enforcement agencies. The Washington Post first reported the existence of the memo.
In it, Mr. Kelly did not directly address the case of the aide, Rob Porter, who was forced out of his job as the White House staff secretary this month after news reports that his two former wives had claimed physical and emotional abuse by Mr. Porter during their marriages.
The White House has been reeling for more than a week amid shifting explanations of how Mr. Porter was allowed to remain in one of the most sensitive posts there despite the F.B.I.’s discovery months ago of the abuse allegations.
The deepening scandal called into question the administration’s veracity as Republicans and Democrats pressured Mr. Kelly to detail what had happened. The memo does not do that.
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But Mr. Kelly’s pledge of action comes after bipartisan pressure from lawmakers on Capitol Hill, who have in recent days demanded that the White House account for Mr. Porter’s case and the broader issue of people without permanent security clearances working at 1600 Pennsylvania Avenue.
“The committee is investigating the policies and processes by which interim security clearances are investigated and adjudicated within the executive branch,” Representative Trey Gowdy, Republican of South Carolina and the chairman of the House Oversight Committee, wrote this week.
Mr. Kelly said that he was putting into effect changes that would address a failure of communication between the F.B.I. and senior officials in the West Wing — exactly the kind of failure that White House officials have said was responsible in Mr. Porter’s case.
Among the most significant changes, Mr. Kelly ordered that F.B.I. officials would now directly report to the White House counsel, Donald F. McGahn II, any concerns that they uncovered during the background investigations of the president’s top aides.
Mr. Kelly said that would ensure that “critical material will be differentiated from the ordinary volume of communications and delivered quickly and directly to the appropriate person rather than through layers of intermediaries.”
Sarah Huckabee Sanders, the White House press secretary, had suggested this week that if changes were necessary in the background check process, it was the responsibility of the F.B.I. to make them.
“If changes are thought to be made, that would be made by the law enforcement and intel communities that run that process, not the White House,” Ms. Sanders said Monday.
Mr. Kelly’s memo noted that he met with F.B.I. officials during his review to discuss “their process and our process.” In testimony to lawmakers on Tuesday, Christopher Wray, the F.B.I. director, said that he was “quite confident that in this particular instance, the F.B.I. followed established protocols.”
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White House officials had earlier said that they were unaware of the allegations against Mr. Porter because the F.B.I. had reported their concerns to a security office staffed by career officials who did not communicate to the West Wing.
People familiar with the background check and security clearance process in prior administrations have said that such communication failures would not — and did not — occur previously because of procedures that were in place.
The changes that Mr. Kelly has ordered suggest that the process for reviewing background investigations and deciding about security clearances had all but broken down during the first year of the Trump administration.
He said that the White House should “develop and implement written protocols governing the review of security files,” suggesting that such written guidelines did not exist.
Mr. Kelly said that the F.B.I. should communicate “significant derogatory information” about a White House employee in 48 hours — an admission that it has taken much longer than that since Mr. Trump became president.
In the future, Mr. Kelly wrote, access to “certain highly classified information” will be kept from people with only interim security clearances unless they receive “explicit” approval from his office, and then only “in the most compelling circumstances.”
That is an admission that too much highly classified information has been shared with Trump administration officials in the White House who had not received permanent security clearances.
Mr. Kelly’s memo makes clear that the White House was aware of shortcomings and concerns with the granting of security clearances several months before Mr. Porter’s case became public this month.
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In September, Mr. Kelly wrote, he ended the practice of granting new interim security clearances without “extraordinary circumstances and my explicit approval.”
He also said that he conducted a review of all White House staff with security clearances, and in some cases reduced the level of clearances for employees who did not need access to classified materials or secret documents.
“I have insisted that we enforce the necessary safeguards and processes to review an individual’s suitability for employment at the White House before that individual begins work,” Mr. Kelly wrote.
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