Washington (CNN) -- In the end, even Eric Shinseki knew he had to go, President Barack Obama said Friday in announcing the resignation of his only Veterans Affairs secretary over a growing scandal involving sometimes deadly waits for care at VA hospitals.
Obama went before reporters shortly after meeting with Shinseki at the White House and said the retired Army general told him that "the VA needs new leadership" to address the widespread problems chronicled in new reports this week, adding that Shinseki "does not want to be a distraction" to fixing the situation.
"That was Ric's judgment on behalf of his fellow veterans, and I agree. We don't have time for distractions. We need to fix the problem," Obama said.
Calls for Shinseki's resignation snowballed in recent days from across the political spectrum -- Republicans and Democrats, as well as veterans' advocacy groups -- because of the misconduct that gained prominence after CNN began reporting problems at VA facilities in November.
Before meeting Obama, Shinseki announced a series of steps intended to address the VA problems, including the removal of senior leaders at the Phoenix VA hospital and elimination of performance awards for VA leaders in 2014.
He also apologized to veterans and Congress, but declared: "This situation can be fixed."
Shinseki then went to the White House to present Obama with findings from his internal audit of what was happening in the VA system, a document that effectively ended his job. He left after the meeting without comment.
The new report found indications that many of the audited facilities had "questionable scheduling practices" that signaled a "systemic lack of integrity" within some VA health facilities.
In announcing Shinseki's resignation, Obama said there was "a need for a change in culture" at veterans hospitals "and perhaps the VA as a whole" to make sure that problems and "bad news" don't get covered up, but get reported and fixed.
He praised Shinseki's service as a soldier "who left part of himself on the battlefield," and a VA leader who helped increase the budget and services, whittle down a backlog of benefits claims and help homeless veterans.
Read Obama's statement
However, the findings of the internal VA report as well as a previous preliminary report by the VA inspector general revealed systemic problems that Obama called "totally unacceptable."
He named a Shinseki deputy, Sloan Gibson, to temporarily assume the VA leadership until a new secretary is named and confirmed.
Political leaders applauded the resignation Friday, but said new leadership must resolve VA shortcomings.
"The denial of care to our veterans is a national disgrace, and it's fitting that the person who oversees the Department of Veterans Affairs has accepted responsibility for this growing scandal and resigned," Senate Republican leader Mitch McConnell of Kentucky said in a statement.
Sources allege secret VA waits lists in Phoenix
Problems in the VA system date back decades, but CNN's reporting of long waits at VA hospitals brought the issue into national focus at the end of 2013. An April report by CNN in which sources said 40 veterans died at a Phoenix VA facility that used secret waiting lists to cover up the problem prompted angry calls for action.
The latest report by the VA inspector general's office and Shinseki's auditors indicated a link between employee bonuses and covering up patient wait times.
Facing mounting calls to resign, Shinseki told a veterans group Friday morning that he was shocked by the inspector general's report, especially the prevalence of wait lists for veterans needing medical care.
"That breach of integrity is irresponsible, it is indefensible and unacceptable to me," he told the National Coalition for Homeless Veterans. "I said when this situation began weeks to months ago and I thought the problem was limited and isolated because I believed that. I no longer believe that. It is systemic."
Shinseki, who has been VA chief for more than five years, said he was misled by others.
"I was too trusting of some, and I accepted as accurate reports that I now know to have been misleading with regard to patient wait times," he said. "I can't explain the lack of integrity among some of the leaders of our health care facilities. This is something I rarely encounter during 38 years in uniform and so I will not defend it because it's indefensible, but I can take responsibility for it and I do."
Among other changes he announced: eliminating wait times as a way to evaluate supervisors' performance, accelerating administration of care to veterans, and asking Congress to fill VA leadership vacancies quickly.
He received a standing ovation at the beginning and end of his appearance.
In the latest accusation against the agency, Reps. Mike Doyle and Tim Murphy of Pennsylvania issued a statement saying 700 veterans had been placed on a primary care waiting list for doctor appointments at the Pittsburgh VA center, with some waiting since 2012.
Such continuing revelations prompted the rising tide of resignation calls, with Democratic legislators facing re-election battles in November pressuring Obama to take action.
"The inspector general's preliminary report makes it clear that the systemic problems at the U.S. Department of Veterans Affairs are so entrenched that they require new leadership to be fixed," said Mark Udall of Colorado, the first Senate Democrat to call for a change at the top.
List of senators calling for Shinseki resignation
Calls for criminal investigation
There also have been calls for a criminal investigation into fraudulent record-keeping to cover up delays at VA hospitals. Obama said Friday that would be up to the Justice Department.
White House spokesman Jay Carney told reporters Thursday that Obama was waiting for the VA internal audit from Shinseki before deciding whom to hold accountable.
He stopped short of saying Obama had confidence in the secretary, pointing instead to the President's recent statement that Shinseki would likely not be interested in continuing to serve if he believed he let veterans down.
In announcing the resignation, Obama sought to honor Shinseki's record of service while insisting the top priority was resolving problems faced by veterans seeking care.
"This issue of scheduling is one that the reporting systems inside of the (VA) did not surface to the level where Ric was aware of it, or we were able to see it," Obama said. Now the task is to get care to veterans waiting for it and figure out how to prevent such delays and cover-ups from recurring, he said.
"How do we make sure that there's no slippage between somebody making a phone call and then getting an appointment scheduled," the President said. "And let's have a realistic time for how soon they're going to get an appointment. Those are things that don't require rocket science. It requires execution. It requires discipline. It requires focus."
Meanwhile, a VA whistleblower who told CNN about the problems at the Phoenix facility said Friday he was saddened by Shinseki's resignation under such circumstances.
"The VA administrators got way too focused on having good numbers and they forgot the most important mandate, the reason we all work at the VA -- to take care of veterans, to save their lives and give them good medical care," Dr. Sam Foote said.
"The next secretary's biggest challenge will be to get that re-focused and make sure the number one job is taking care of veterans - not worrying about their bureaucratic careers," Foote added.
The preliminary inspector general's report made public Wednesday described a "systemic" practice of manipulating appointments and wait lists at the Veterans Affairs Medical Center in Phoenix.
According to the report, at least at least 1,700 military veterans waiting to see a doctor were never scheduled for an appointment or were placed on a waiting list at the Phoenix VA, raising the question of just how many more may have been "forgotten or lost" in the system.
Breaking the scandal
CNN exclusively reported the situation in Phoenix last month, and obtained an e-mail written by an employee at a Wyoming VA clinic that said staff was instructed to "game the system" to make the clinic appear more efficient.
The VA's troubled history
Shinseki finds himself in a firestorm
The VA has acknowledged 23 deaths nationwide due to delayed care. As political pressure ratcheted up this week, Shinseki sought to get ahead of it in an opinion piece published Thursday in USA Today that said he's "not waiting to set things straight."
"I immediately directed the Veterans Health Administration ... to contact each of the 1,700 veterans in Phoenix waiting for primary care appointments in order to bring them the care they need and deserve," Shinseki wrote.
Shinseki reiterated other steps he's taken, including ordering a "nationwide audit of all other major VA health care facilities to ensure understanding of, and compliance with, our appointment policy."
His further steps announced Friday, while targeted at the core of the problems, proved too little too late to save his job.