Mr. Porter’s former wives have said the F.B.I. interviewed them about their abuse claims in January 2017. Mr. Porter himself also alerted Mr. McGahn that an aggrieved ex-wife was making potentially damaging accusations about him, according to a person familiar with the discussion. Mr. Roberts’s letter says that in August, the bureau received a request from the White House personnel security office for additional information on Mr. Porter, “including, but not limited to, re-interviews of Mr. Porter, his ex-wives and his girlfriend at the time.”

In November, the F.B.I. gave the White House another report, Mr. Roberts wrote, “which contained additional derogatory information.”

The F.B.I.’s timeline is at odds with the one given by top officials including John F. Kelly, the White House chief of staff, who acknowledged in March that he had stumbled in his response to the allegations against Mr. Porter but insisted that he had not known of the damaging accusations until the week Mr. Porter left.

Background investigations often uncover derogatory information, and one person familiar with Mr. Porter’s said the allegations of abuse and the circumstances surrounding them were not as clear-cut as they were portrayed to be when they surfaced in the press, making it difficult to discern whether they warranted action. Even though the White House now appears to have known for months about the claims against Mr. Porter, his temporary clearance was never revoked.

The White House’s contention that Mr. McGahn never saw the original F.B.I. report comes as it is facing fresh questions about its process for vetting personnel for top posts in Mr. Trump’s administration, after Dr. Ronny L. Jackson, the White House physician who was his pick to be the secretary of veterans affairs, withdrew on Thursday amid damaging allegations that he drank on the job, overprescribed medication and presided over a hostile work environment.

Like Dr. Jackson, Mr. Porter was among a small circle of senior officials who spent their days in proximity to Mr. Trump. As staff secretary, Mr. Porter handled the reams of sensitive documents that flow through the president’s office daily. The allegations against him were one reason he could not obtain a permanent security clearance, and the scandal surrounding his departure highlighted a pattern at the White House of allowing senior officials who had not been given permanent clearance to see classified information to serve in the highest echelons of the White House.