Veterans Affairs Secretary Eric Shinseki announced Friday he was removing the leadership at the Phoenix VA hospital and shortly afterward tendered his resignation to President Obama.
The president said he had regretfully accepted. Deputy VA Secretary Sloan Gibson will serve in the interim.
"Ric's commitment to our veterans is unquestioned. I am grateful for his service," Obama said.
Shinseki apologized for the health care agency's problems all across the country. At least 40 patients may have died as a result of mismanagement at the Phoenix hospital. Director Sharon Helman and two subordinates had been placed on administrative leave in early May.
"I've initiated the process for the removal of the senior leaders at the Phoenix VA medical center," Shinseki told a group of veterans in a meeting in Washington. The announcement was met with applause.
Shinseki did not mention names or how many people would lose their jobs.
"We will use all authority at our disposal and force accountability among senior leaders who have been found to have instigated, tolerated dishonorable or irresponsible scheduling practices at VA health care facilities," Shinseki said.
The embattled retired four-star general also said that there would be changes made to appointment procedures.
Obama and Shinseki talked at the White House after the meeting with the veterans. At a press conference later, the president said that Shinseki had ordered the VA to "contact every veteran in Phoenix waiting for appointments to get them the care they need and deserve."
President has accepted Sec. Shinseki's resignation. Good move. Now let's fix the problems. #VA— Jeff Flake (@JeffFlake) May 30, 2014
Sen. John McCain, a veteran and one of Shinseki's most vocal opponents, said the resignation was "the right move" and called for a stronger VA.
"New leadership at the VA is just the first step in what must be a significant, sustained effort by Obama to fix its systemic problems," he said in an emailed statement. "The president must join with Congress to support legislation we will introduce next week to strengthen the ability of VA administrators to hire and fire those charged with providing care and, most importantly, give far greater flexibility to veterans to get the care they need and deserve, where and when they want it."
Earlier this week, the Inspector General filed a report that confirmed allegations of excessive wait times for appointments and staffers who falsified data. Patients waited an average of 115 days for a first appointment. The hospital had reported a 24-day wait for an initial visit.
In resigning, the secretary told Obama the agency needed new leadership and he didn't want to be a distraction. "I agree. We don't have time for distractions. We need to fix the problem," Obama said.
The Associated Press contributed to this article.