By Maggie Haberman and Katie Rogers

New York Times News Service

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 the Trump administration. He frequently travels with President Donald Trump on Air Force One, and he helped write Trump’s first State of the Union address last month.

But despite initial support from John Kelly, the White House chief of staff, and other West Wing staff aides, 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 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, Porter said “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.

The White House’s initial response was consistent with how both Trump and his aides have handled allegations of harassment or abuse against the president or his allies and advisers since the 2016 presidential campaign. Trump vigorously defended Roy 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, Porter, 40, had been widely regarded as a rising star. A Harvard graduate, Rhodes scholar and former Senate aide, Porter was an ally of 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, Porter did not have the permanent security clearance that aides of his rank always have.

Willoughby, Porter’s second wife, said in an interview Wednesday that when the FBI was conducting research for Porter’s security clearance, he asked her whether she had told investigators about their marriage.

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

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

In addition to asking her about what she said to FBI officials, Porter, she said, had been in touch several times over 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, Virginia, court, Willoughby accused Porter of growing angry when she said he had violated a private separation agreement. A day later, her complaint said, Porter entered her apartment with a key he had not given back.

According to her complaint, Porter left only after 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,” Willoughby wrote in the complaint, “he apologized and begged me not to involve them.”

Holderness, 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, Holderness has a blackened right eye and a swollen cheekbone.

In his statement, Porter said the pictures of 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 several statements to The Mail on Tuesday evening in support of Porter. In one, Kelly, who in recent months has leaned heavily on Porter in his efforts to bring order to a chaotic West Wing, called 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,” Kelly said. “I am proud to serve alongside him.”

But by Wednesday evening, after reports that Kelly had known since the fall about the nature of the allegations against Porter, Kelly issued a statement indicating that was not the case.

“I was shocked by the new allegations released today against Rob Porter,” Kelly said in the statement. “There is no place for domestic violence in our society. I stand by my previous comments of the Rob Porter that I have come to know since becoming chief of staff, and believe every individual deserves the right to defend their reputation. I accepted his resignation earlier today, and will ensure a swift and orderly transition.”

Several aides said they were confused as to why Kelly and others so forcefully defended Porter initially.

Two White House officials, who asked not to be identified because they were not authorized to speak about the internal deliberations, insisted that Porter had misled Kelly and several other aides about the severity of the allegations. He had portrayed the women as making up stories to cause trouble, and few, if any, aides in the White House considered conducting their own investigations to discover what might have taken place, the officials said.

After initially saying that Porter would remain on for a period of time, one of the White House officials said that he would be gone by the end of the week, as the West Wing faced blowback for standing by him.