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President Obama on Friday accepted the resignation of Veterans Affairs Secretary Eric Shinseki, saying that the cabinet official “does not want to be a distraction” from fixing the problems at the embattled agency.

The president acted after more than 100 members of Congress called for Shinseki’s ouster. But veterans groups said that Shinseki’s departure alone is not enough to address longstanding institutional problems at the Department of Veterans Affairs, which includes the widespread scandal of veterans not receiving timely care at a Phoenix hospital an issue that’s been called “systemic” by an independent report.

“Secretary Shinseki didn't bring these problems with him, and they won't go away if he leaves; the president is ultimately responsible for ensuring that the department is fixed,” Derek Bennett, chief of staff of Iraq and Afghanistan Veterans of America (IAVA), told Fusion. “The American people need to be vigilant until that happens.”

Obama announced that deputy VA secretary Sloan Gibson will serve as acting head of the agency. The IAVA said in statement that it is “standing by to support” Gibson, but Bennett acknowledged Gibson faces a daunting task of addressing the administration’s problems, which are “clearly systemic and likely grounded in culture.”

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An interim inspector general (IG) report released this week found that 1,700 veterans were waiting for care at the Phoenix VA hospital alone, but were never placed on official electronic wait lists, meaning that “these veterans were and continue to be at risk of being lost or forgotten.”

The IG report studied 226 veterans at the Phoenix hospital, and the results showed that they waited an average of 115 days to be seen for their first appointment, even though official records indicated wait times only averaged 24 days.

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The problems in Phoenix first emerged last month when a retired VA physician turned whistleblower, Dr. Samuel Foote, alleged that up to 40 veterans died while waiting for as long as 21 months to be seen for treatment. The inspector general is investigating whether their deaths were a direct result of not being seen by a physician.

Foote said in an interview Friday that Obama had no choice but to accept Shinseki’s resignation, but that the VA’s bureaucracy, and not just the secretary or the president, was to blame for the scheduling scandal.

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“Fighting a gigantic bureaucracy that runs like a fraternity or sorority with secret handshakes or whatever, you’ve got a group really tied together, and trying to change that culture is going to [be] a tremendous task,” he said.

Issues with improper scheduling practices are not new at the VA, according to the most recent inspector general report. Since 2005, the IG has issued 18 reports on scheduling problems at clinics across the country, resulting in long wait times and deficient patient care.

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Obama himself alluded to those persistent issues on Friday, saying that, “the VA is a big organization that has had problems for a very long time.”

“There is a need for a change in culture within the VHA and perhaps … the VA as a whole, that makes sure that bad news gets surfaced quickly, so that things can be fixed,” the president said.

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Before tendering his resignation, Shinseki and deputy White House chief of staff Rob Nabors led a review of VA healthcare facilities. Obama said Friday that Shinseki had “begun the process” of firing senior officials at the Phoenix VA, canceling performance bonuses for senior VA healthcare officials, and getting treatment for veterans waiting for care in Phoenix as soon as possible.

Shinseki himself announced the changes this morning during a speech to the National Coalition of Homeless Veterans, his last speech as secretary.

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The House of Representatives went one step further, passing a bipartisan bill last week that would make it easier for senior VA officials to be fired. The Senate has yet to take up the measure, and the Obama administration has objected to it, saying it could result in litigation from unions and associations representing VA employees.

Veterans groups said they are looking not just for changes in management, but significant reforms to how the VA operates.

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“America's vets are looking to the commander in chief to act quickly,” IAVA founder and CEO Paul Rieckhoff said in a statement. “President Obama must move now to appoint an energetic secretary who is unafraid to make bold changes and work quickly and aggressively to change the VA system.”

Jordan Fabian is Fusion's politics editor, writing about campaigns, Congress, immigration, and more. When he's not working, you can find him at the ice rink or at home with his wife, Melissa.