The problems at Veterans Affairs extend well beyond long wait lists, with a report Tuesday showing the department is plagued with poor care that has cost up to 1,000 veterans their lives and left taxpayers on the hook for nearly $1 billion in malpractice settlements since the beginning of the wars in Iraq and Afghanistan.

Some of the problems detailed in the report by Sen. Tom Coburn of Oklahoma are downright ghoulish. They include the case of a former security chief at a New York Veterans Affairs medical center whom the FBI arrested on charges of plotting to kidnap, rape and murder women and children.

More standard is the nightmarish bureaucratic bungling that shows a department in disarray and a culture more concerned with punishing whistleblowers than with fixing the problems they pointed out, said Mr. Coburn, Senate Republicans’ chief investigator who has earned a reputation as the top waste-watcher in Congress.

“The problems at the VA are worse than anyone imagined,” Mr. Coburn said. “Over the past decade, more than 1,000 veterans may have died as a result of VA’s misconduct and the VA has paid out nearly $1 billion to veterans and their families for its medical malpractice.”

The VA has come under fire in recent months over reports that dozens of veterans died while stuck on secret waiting lists at a VA facility in Phoenix. Since then, an inspector general’s investigation has found widespread misuse of secret wait lists in a number of facilities. The department’s secretary has resigned.

But Mr. Coburn’s report, titled “Friendly Fire: Death, Delay and Dismay at the VA,” argues that problems go back well before the Phoenix scandal and run deeper than bogus wait lists and scheduling practices designed to help managers show that they are meeting performance goals.

His exhaustive study, which combines previously reported problems and some new ones, highlights horrifying cases.

One involves a Philadelphia veteran who went in for a tooth extraction. Doctors went ahead with the procedure despite his dangerously low blood pressure. On his way home from the operation, he had a stroke and was left paralyzed.

Another veteran had annual chest X-rays, but doctors never spotted a growing lesion in his lung. It ultimately killed him.

A veteran in South Carolina had to wait nine months for a colonoscopy. By the time he underwent the procedure, cancer was diagnosed at stage three. In that case, the VA admitted that had he been treated earlier, his case might not have been as severe, Mr. Coburn said.

Mr. Coburn’s report appears to reject the claims of some VA defenders who acknowledge that problems exist but say they shouldn’t tarnish the image of care the health system provides.

Some lawmakers on Capitol Hill have said the VA problems will need to be solved with an infusion of funds.

But Mr. Coburn traced the problem to bad management and lax working standards, not to lack of money. In one finding, he said VA doctors average about half the workload that private-practice primary care physicians do, suggesting there is room for them to take more patients.

Among his other findings:

• Female patients received unnecessary pelvic and breast exams from a sex offender.

• Delays are endemic. In addition to care waiting lists, the VA is behind on processing disability claims and constructing facilities.

• Some VA health care providers have lost their medical licenses, but the VA hides that information from patients.

• The federal government has paid out $845 million for VA medical malpractice settlements since 2001.

Mr. Coburn included a photo from one VA facility in North Carolina that couldn’t find proper storage for 37,000 benefit claim folders. They were piled on top of filing cabinets, apparently in random order, making it not only poor case management, but also a fire hazard, Mr. Coburn said.

In the stunning case of the police chief, Richard Meltz, head of security at the Bedford VA Medical Center, pleaded guilty in January to involvement in what the FBI called “two sadistic kidnapping, rape and murder conspiracies.” Meltz advised two others on how to avoid being tracked, such as not using toll roads, and where to dump bodies, according to the FBI.

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