WASHINGTON — Eric Shinseki resigned as secretary of the Veterans Affairs Department Friday after meeting face-to-face with President Obama about mounting evidence of widespread misconduct and mismanagement at the agency’s vast network of medical facilities.

In a statement Friday morning after the meeting, Mr. Obama said that Mr. Shinseki had offered his resignation from the post he has held since the beginning of the president’s administration. “With regret, I accepted,” Mr. Obama said.

“He has worked hard to investigate and identify the problem,” the president said, adding that Mr. Shinseki told him that “the V.A. needs new leadership to address it. He does not want to be a distraction.”

Mr. Shinseki, 71, had said for weeks that he wanted to stay in his job to confront accusations that officials at the department’s hospitals had manipulated waiting lists to cover up long delays in scheduling appointments for thousands of veterans.

In a speech Friday morning to a veterans group, he apologized and described his agency as having “a systemic, totally unacceptable lack of integrity.” He vowed to fix what he called a “breach of integrity” and said he had already initiated the firing of top managers at the V.A. medical center in Phoenix, where allegations of mismanagement first surfaced.

Shinseki had to go because he was incompetent at hiding incompetence.

— David Burge (@iowahawkblog) May 30, 2014