As the White House staff secretary, Rob Porter is not a public figure, but he is responsible for paper flow to the president, a job of crucial importance in the Trump administration. He frequently travels with President Trump on Air Force One, and he helped write Mr. Trump’s first State of the Union address last month.

But despite initial support from John F. Kelly, the White House chief of staff, and other West Wing staff aides, Mr. Porter announced his resignation on Wednesday, a day after his two former wives accused him in interviews of physical abuse when they were married to him.

His troubles were not a complete secret at the White House: Two people close to the White House said that the allegations against him made by his former wives, Colbie Holderness and Jennifer Willoughby, had contributed to a delay in granting him a permanent security clearance.

In a statement, Mr. Porter said that “these allegations are simply false,” even as details of the alleged abuse and photographs of one of his former wives with a black eye that she said he had given her were widely circulated.

The White House’s initial response was consistent with the way both Mr. Trump and his aides have handled allegations of harassment or abuse against the president or his allies and advisers since the 2016 presidential campaign. Mr. Trump vigorously defended Roy S. Moore, the failed Alabama Republican Senate candidate, against allegations that included child molestation, and Sarah Huckabee Sanders, the White House press secretary, has said that multiple women who have accused the president of sexual misconduct were lying.

In the White House, Mr. Porter, 40, had been widely regarded as a rising star. A Harvard graduate, Rhodes scholar and former Senate aide, Mr. Porter was an ally of Mr. Kelly’s and a steady force in a West Wing populated by aides vying for face time with — and influence over — the president. But, a year into his job, Mr. Porter did not have the permanent security clearance that aides of his rank always have.

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