“Interim clearance is simply to allow people to operate for a short time in their jobs while they await a full check, but if you get red flags in that interim clearance process, then it means that you shouldn’t have that interim clearance,” he added.

Even as Mr. Kelly’s past efforts to deal with security clearance issues at the White House were becoming clearer, his shifting public responses to the revelations of Mr. Porter’s past were coming under further scrutiny.

Three people briefed on the situation said that Mr. Kelly learned that the accusations would be published in The Mail last Tuesday, before leaving for a visit to Capitol Hill. In a meeting with a group of aides, including several from the press office, everyone agreed that Mr. Porter would have to resign, the people briefed on the situation said, and a statement from Mr. Kelly was drafted to provide to The Mail.

But Mr. Porter continued to deny the accusations from his former wives. One aide in the discussions pushed back on the belief that Mr. Porter should resign, saying that these were mere allegations, and that if Mr. Porter were forced out over them, other people could be forced from their posts any time an allegation was made. Other aides agreed, and argued for waiting for the story to play out.

At that point, they reached out to Mr. Kelly, who had left for the visit to the Capitol, by phone, the people said, and he said he agreed, telling them to make his statement about Mr. Porter more supportive. Mr. Kelly dictated specific language that he wanted in the statement to Sarah Huckabee Sanders, the White House press secretary.

A short time later, The Mail published Mr. Kelly’s statement calling Mr. Porter “a man of true integrity and honor,” someone with whom he was “proud to serve,” and who had faced “vile” accusations from his former wives.

But soon after the article appeared, Mr. Kelly, who by then had returned to the White House, heard from someone with more detailed knowledge of the allegations against Mr. Porter that more damning information was about to come out, and that the chief of staff should not put himself in the position of being Mr. Porter’s main defender. The people briefed on the discussions would not identify that person.