Few institutions have such noble origins as the Department of Veterans Affairs, which can trace its mission to Abraham Lincoln’s Second Inaugural Address. On March 4, 1865, the careworn leader affirmed that among the nation’s highest moral obligations were “to care for him who shall have borne the battle and for his widow and his orphan.’’

Those words have adorned the VA’s Washington, D.C., headquarters for more than 50 years. But an appalling new report released this week suggests that Lincoln’s message was lost on far too many of those who run the VA’s hospitals and clinics.

The interim report from the VA’s Office of Inspector General, focused on the Phoenix veterans health care system, found that wait times for primary-care appointments were longer than initial reports suggested, with 1,700 veterans not even on the official waitlist.

Even more alarming, the report suggests that inappropriate scheduling, which can lead to delayed care, may be a “systemic’’ deficiency.

The inspector general has dispatched “rapid response” teams to determine the depth of the problems nationwide, including whether veterans have died because they were kept waiting. Investigators also are working with the U.S. Department of Justice to determine if there’s sufficient evidence to hold the “VA or specific individuals accountable on the basis of criminal, civil or administrative law and regulations.” A chief concern is that wait times might have been covered up so that staff qualified for advancement or bonuses.

The full-throated outrage sparked by this report is merited, though it’s worth noting that initial data provided by Minnesota’s regional VA system suggests that it’s run much more responsibly. Still, deeper investigation is needed here and elsewhere. The Phoenix mismanagement is a national disgrace. Scrutiny is needed to ensure that the agency and those it serves have not been betrayed elsewhere at such a crucial time.

The VA is rapidly trying to retool for younger generations of veterans who served in Iraq and Afghanistan. Thanks to body armor and advanced medical care, many survived serious wounds that would have killed soldiers in the past. Their care challenges — disabilities, traumatic brain injuries and mental health needs that are taken more seriously than in previous eras — are distinct from the World War II generation’s age-related conditions that the agency is accustomed to.

Younger veterans need confidence that this next-generation system is ready and that it puts their needs first. A first step in rebuilding the broken public trust is new leadership. VA Secretary Eric Shinseki, a retired U.S. Army four-star general, has served this country with honor for decades, but the VA mess happened on his watch. His resignation Friday was appropriate, yet further housecleaning is needed.

The political outrage also needs to yield meaningful action. The bipartisan blasting of alleged VA mismanagement ought to have Congress uniting around a bill that Vermont Sen. Bernie Sanders is reviving. The legislation would expand benefits and add up to 27 new VA health care facilities to help address the care backlog. Despite backing by just about every veterans’ advocacy group, the landmark bill was blocked in February by Senate Republicans for being too costly.

With the spotlight on the VA, this also is a time to ask broader questions about its future. One that ought to get a high-profile airing was asked during 1990s health reform efforts. Should the VA remain a separate system or should it morph into a system like Medicare, which covers care for seniors but relies on private-sector providers and hospitals?

Some congressional Republicans are making timely calls to have veterans rely more on care from private providers (the VA recently expanded options to do so, but avenues are still limited). While some see this as an ideological push to dismantle the VA, the idea shouldn’t be dismissed out of hand. Private providers also can have access problems, but moving closer to a Medicare model could help address VA care backlogs and provide care closer to veterans’ homes. A hybrid approach — that keeps the VA as a specialty care mainstay but that shares much more of its primary care demands with private providers — is worthy of serious consideration.