If you thought the Obama administration had put its problems with veterans behind it, think again.

Two years after the scandal emerged over phony waiting lists for patients at the Department of Veterans Affairs facility in Phoenix, the department is still beset with problems ranging from fresh accusations of falsified waiting lists to a system-wide failure to discipline wrongdoing.

“The VA is still struggling with a lack of accountability, an inability to properly manage a budget rapidly approaching $200 billion, and a failure to provide veterans with timely access to care and benefits,” said John Cooper, a spokesman for Concerned Veterans for America. “The VA is broken, and if we want veterans to be assured of a VA that works, we need to systemically reform it.”

Employee discipline has become an embarrassment. Even in the rare cases where VA management does punish employees, the agency is being thwarted by union-backed civil service rules.

For example, a VA employee in Puerto Rico was reinstated with back pay last month after she was fired upon being arrested for armed robbery. She pleaded guilty, but her union got her job back by arguing in a grievance that a VA manager at the facility is a registered sex offender and another VA hospital manager was once arrested for drunken driving and found in possession of pain pills.

In Alexandria, Louisiana, a VA nursing assistant is still on the payroll while awaiting trial on manslaughter charges in the death of a 70-year-old Air Force veteran in 2013. Hospital officials initially called the veteran’s death an accident, but a coroner determined the veteran died from blunt force trauma to the head.

House Committee on Veterans’ Affairs Chairman Jeff Miller, Florida Republican, said the case is an example of “VA’s continued and pervasive failure to seriously discipline its employees.” The agency has said civil service rules make it difficult to fire poor-performing employees and has recommended changes to Congress.

Mr. Cooper said it’s taken the VA two years to propose firing three senior leaders responsible for the Phoenix VA scandal, “which led to nearly 300 veterans dying waiting for care.”

The VA didn’t respond to requests for comment.

The agency’s problems go far beyond civil service rules, however.

The agency’s inspector general released twelve reports on VA health care systems in Texas last month, revealing that seven of them have scheduling mismanagement that led to extended wait times for veterans. The reports blamed that lack of supervision, poor training of employees and weak management controls for data manipulation.

In San Diego, California, the inspector general reported Friday that staff at the Veterans Affairs Medical Center manipulated waiting list data to make it appear veteran patients received mental health care more quickly than they actually did. The report covered fiscal 2012 and 2013.

The department’s inspector general told USA Today in February it has investigated 73 VA facilities across the country, and found scheduling problems in 51 cases. But the inspector general still has not released reports with the findings of nearly all those investigations to Congress or the public.

In Denver, the VA said it has no plans to punish any other employees over massive cost overruns at the VA medical facility under construction. The executives responsible for the cost of the project rising to $1.7 billion have already left the department, the agency said in an internal review, while three other executives were transferred or demoted.

In Jackson, Mississippi, an investigation found that taxpayers are paying millions for VA hospitals to keep health care workers with questionable records on paid leave for years. The Clarion-Ledger reported in February that two surgeons at the G.V. “Sonny” Montgomery VA Medical Center whose annual salaries total more than $500,000 have been on paid leave more than two years. Their salaries count against the Jackson VA’s budget, but veterans receive no care from them.

The paper found that 2,560 VA employees spent at least one month on paid leave in 2014, costing taxpayers $23 million — more than any other federal agency. VA Secretary Robert McDonald said the agency is streamlining the administrative leave process so employees can be disciplined more quickly.

In Clarksburg, West Virginia, veteran Terry Riley has filed suit against the Louis A. Johnson VA Medical Center, alleging that the facility has “a practice of falsifying and reducing emergency room numbers.” His claim accuses the facility’s managers of “utilizing false clinics to enable senior managers to reduce ER visits and receive a high yearly bonus,” against VA policy.

The VA last month did take disciplinary action against one notable employee. The agency suspended the head of the Veterans Benefits Administration Danny Pummill for allowing two lower-ranking officials to manipulate the agency’s hiring system for their own gain.

Mr. Pummill was suspended without pay — for 15 days. Deputy VA Secretary Sloan Gibson said Mr. Pummill failed to exercise proper oversight as Kimberly Graves and Diana Rubens forced lower-ranking managers to accept job transfers and then stepped into the vacant positions themselves, keeping their senior-level pay while reducing their responsibilities.

But Ms. Graves and Ms. Rubens were reinstated last month after administrative judges overturned their firings. The agency reprimanded them and cut their pay by 10 percent.

Last week, Sen. Marco Rubio, Florida Republican, and Mr. Miller wrote to Senate Committee on Veterans’ Affairs Chairman Johnny Isakson, Georgia Republican, to warn that failure of Congress to pass new language allowing the VA to fire corrupt or negligent officials would be a “disservice” to the nation’s veterans. They urged him to consider Mr. Miller’s bill, which would expand the agency’s authority to fire employees.

“We are now concerned that you have halted the aforementioned negotiations and may be taking an approach that favors reaching a deal with the administration or others at any cost, regardless of whether it actually addresses the VA’s many problems or pays for new programs in a responsible way,” the lawmakers wrote. “We hope you realize that any piece of comprehensive veterans’ legislation that doesn’t provide the VA secretary swift and comprehensive disciplinary authority for all VA employees misses the true mark on what ails the department.”

Some veterans groups are concerned that the VA’s problems are getting less attention during the presidential election year.

“We are encouraged some of the individuals running for president have been vocal about the plight of our veterans, but what’s more important is that our next commander in chief, regardless of party, commit to reforming the VA and standing up to the special interests that have prevented reforms to the department that would ensure our veterans receive the best care possible,” Mr. Cooper said.

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