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Rob Porter, the White House staff secretary, left, with Stephen Miller, a senior adviser to President Trump, on Monday in Washington. Credit Pete Marovich for The New York Times

WASHINGTON — 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 this White House. 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 on Wednesday, despite support from John F. Kelly, the White House chief of staff, and other West Wing staff aides, Mr. Porter announced his resignation, 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 gave her were widely circulated.

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Mr. Porter did not mention a departure date from the White House, and he still has the president’s support. Sarah Huckabee Sanders, the White House press secretary, said Wednesday that Mr. Trump retained “full confidence” in Mr. Porter’s abilities, making it clear that the official preference was for Mr. Porter to remain in his job, and that it was his choice to leave.

The White House’s response was consistent with how 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 Ms. Sanders has said that multiple women who have accused the president of sexual misconduct were lying.

In the White House, Mr. Porter, 40, was 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.

Ms. Willoughby, Mr. Porter’s second wife, said in an interview on Wednesday that when the F.B.I. was conducting research for Mr. Porter’s security clearance, he asked her if she had told investigators about their marriage.

“He believed that that was holding up his clearance,” Ms. Willoughby said. “I did describe my marriage in detail.”

Ms. Willoughby, who said that she divorced Mr. Porter in November 2013, decided to go public about the allegations after facing pressure from Mr. Porter to issue a statement that she felt “minimized” her experiences in their marriage.

In addition to asking her about what she said to F.B.I. officials, Mr. Porter, she said, had been in touch several times over the course of the past year to urge her to take down a blog post in which she detailed abuse in their marriage without naming him.

According to an emergency protective order she filed in June 2010 against him in an Arlington, Va., court, Ms. Willoughby accused Mr. Porter of growing angry when she said he had violated a private separation agreement. A day later, her complaint said, Mr. Porter entered her apartment with a key he had not given back.

According to her complaint, Mr. Porter left only after Ms. Willoughby had asked him to leave several times. He returned minutes later and “punched in the glass on the door,” trying to get into the apartment. He left the property after she read her name and address aloud to a 911 dispatcher.

“When he heard me on the phone with the police,” Ms. Willoughby wrote in the complaint, “he apologized and begged me not to involve them.”

Ms. Holderness, Mr. Porter’s first wife, described their relationship as “verbally, emotionally and physically abusive” in an interview with The Daily Mail. In photographs she gave to The Intercept, Ms. Holderness has a blackened right eye and a swollen cheekbone.

In his statement, Mr. Porter said the pictures of Ms. Holderness were misleading.

“I took the photos given to the media nearly 15 years ago, and the reality behind them is nowhere close to what is being described,” he said. “I have been transparent and truthful about these vile claims, but I will not further engage publicly with a coordinated smear campaign.”

The White House sent out several statements to The Mail on Tuesday evening in support of Mr. Porter. In one statement, Mr. Kelly, who in recent months has leaned heavily on Mr. Porter in his efforts to bring order to a once chaotic West Wing, called Mr. Porter “a man of true integrity” whom he could not say “enough good things” about.

“He is a friend, a confidant and a trusted professional,” Mr. Kelly said. “I am proud to serve alongside him.”

Asked in her daily briefing what the president thought of the photographs of Mr. Porter’s bruised former wife, Ms. Sanders said she had not discussed them with him, and she declined to discuss specifics about Mr. Porter’s security clearance.

Mr. Porter’s former boss, Senator Orrin G. Hatch, Republican of Utah, sent his own statement to The Mail, saying that the article contained “vile” smears and vouching for Mr. Porter’s character.

But in a new statement on Wednesday, Mr. Hatch said that he was “heartbroken” by the allegations against Mr. Porter, who he said had been a beloved staff member and trusted adviser.

“I do not know the details of Rob’s personal life,” he said. “Domestic violence in any form is abhorrent and unacceptable.”

Aware of Mr. Hatch’s comments, Ms. Willoughby said that she would let her story speak for itself. Ms. Willoughby, who works as a writer and public speaker, said that “this discourse that we’re in in terms of women’s rights and the ‘Me Too’ movement” was a reason for stepping forward, and a reason she agreed with Mr. Porter’s decision to resign.

“Rob is in fact charming and intelligent and diligent and extremely good at his job,” Ms. Willoughby said. “And, in capital letters, abusive and manipulative and toxic in his personal relationships.”

Congressional Democrats have been trying for months to get the White House to provide information about its security clearance process, including how many White House aides have been granted interim clearances because of issues that arose during their F.B.I. background checks.

Representative Sean Patrick Maloney, Democrat of New York, who served as staff secretary to President Bill Clinton, called for the House Oversight Committee to open an investigation into whether Mr. Porter was allowed to access confidential materials without a security clearance, and whether Mr. Kelly had knowledge of the abuse allegations.

“It’s unclear what kind of vetting process was followed in this case,” Mr. Maloney said in a statement.

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