VA Secretary Robert McDonald disputed an audit’s conclusions that his department needs a “systemwide reworking,” saying Wednesday that he’s already fixed many of the problems and what he really needs is a bigger budget and more flexibility to move that money around.

The $68 million independent audit, released last month, said the Department of Veterans Affairs could become a world-class health system if it had better leadership, cut through a bloated bureaucracy and figured out its facilities budget.

But Mr. McDonald, who took over as top leader last year after his predecessor was ousted, said more money would help solve most of the remaining issues.

“The only way forward, if we really want to serve veterans, is for Congress to provide VA with sufficient resources to meet the requirements Congress has set,” Mr. McDonald told the House Committee on Veterans’ Affairs.

His comments are the latest salvo in what’s become a battle over the fate of the VA, which has been damaged by repeated scandals of bad budgeting and secret wait lists that left veterans struggling for care, as clinic officials collected bonuses for making scheduling targets.

Watchdogs and Republicans in Congress say the VA needs a massive shake-up to get beyond those problems, but the administration insisted it’s already on the right path, and said Congress is ignoring those improvements.

“Maybe someday you could hold a hearing on its progress,” Mr. McDonald said. “I’d welcome that.”

But Committee Chairman Jeff Miller, Florida Republican, said Congress has already given the VA a lot of leeway, such as an emergency injection of money this year for a facility in Denver that’s $1 billion over budget. Mr. Miller called that project a “screwup.”

Last month’s independent audit also suggested the Veterans Health Administration, the VA’s medical arm, should consider focusing on specialized care such as amputations, traumatic brain injuries, post-traumatic stress disorder, Hepatitis C and other such ailments instead of trying to handle all types of general health.

The 5.8 million veterans enrolled for VA health care look to the agency for about 50 percent of their care, Brett Giroir, a senior fellow at the Texas Medical Center Health Policy Institute and contributor to the independent study, said. This suggests that they are “voting with their feet” and choosing to seek private care for general health, he said.

Mr. McDonald and his deputy, Dr. David Shulkin, largely disagreed with that notion, saying that the “comprehensive care” the VA provides veterans accounts for more than general health and extends to social services and mental health care.

And Rep. Corrine Brown, ranking Democrat on the committee, said she feared outsourcing all general health care would lead to a push to privatize the VA.

“There are people out there who would want to completely close the VA and privatize the VA system, which is absolutely unacceptable and not what the veterans want,” the Florida Democrat said.

Mr. McDonald said the biggest challenge is hiring enough doctors to care for an increasing number of veterans needing care.

He asked Congress to give him power to shift money around within the department without having to get approval from Capitol Hill first.

The VA has been wrangling with Congress over 2016 spending. The House planned to spend $1.6 billion less than President Obama called for.

Fiscal year 2016 began last week, but the VA and most other agencies are operating on stopgap funding.

Mr. McDonald said more money could help avoid the wait-time scandal that was uncovered last year, which saw staff cancel or hide appointments in order to make it appear they were meeting demands. The secretary said that was a result of a spike in demand for care, and more money and a streamlined hiring process would help.

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