The concerns were first raised in 2011 by Dr. Lisa Nee, a cardiologist at Edward Hines Jr. VA Hospital, just west of Chicago.
Her claims: Veterans were being subjected to unnecessary coronary artery bypass surgeries. She also said that the hospital's echocardiogram laboratory had a one-year backlog and that many patients had died or suffered complications before their echocardiograms were reviewed.
She says her concerns were ignored and she left the VA in 2013. Nee became a whistleblower and took her case to the U.S. Office of Special Counsel, which protects government workers who report damaging information about the agencies where they work.
"I have absolutely no doubt patients died as a result of the care they did not get at the VA Hines facility," Nee told CNN from Chicago, where she now works as chief medical officer for a medical start-up. No VA investigation has made that determination.
In a letter to the White House last week, the Office of Special Counsel said these issues were largely substantiated by VA officials, but then not satisfactorily addressed.
The letter also described a "lack of accountability," stating that the VA's medical inspector identified repeated errors by one physician without taking any disciplinary action. The physician is still at Hines.
The letter noted that reports by VA agencies "confirm deficiencies in cardiovascular care."
A VA Inspector General report released in February confirmed that more than 1,200 cardiology tests were delayed in 2014 at the Hines VA, with some wait times of more than 120 days.
This caused a delayed diagnosis for at least one patient who required surgery, but the report concluded that "no apparent adverse effects occurred."
A separate report from the Inspector General in 2014 found heart procedures at the facility "may have been inappropriate" for nine patients and confirmed other problems involving medical evaluations, equipment quality and the availability of hospital beds.
But the IG report did not find evidence of actual harm to patients.
In her conclusion, the head of the Office of Special Counsel, Carolyn Lerner, said: "I do not find reasonable the VA's conclusion that none of the findings constitutes a substantial and specific danger to public health or safety."
In a statement to CNN, the VA Inspector General said: "These reports include recommendations to VA that we believe will address the issues that are substantiated. We keep the reports open until we have assurances that VA has satisfactorily fulfilled their commitments to implement the recommendations."
The Office of Special Counsel's letter says the VA took some corrective actions, but added that Nee had raised unresolved issues.
A Hines VA spokesperson said in a statement to CNN that the facility has hired additional cardiologists and responded to recommendations by the Inspector General by changing diagnostic and post-procedure review processes.
"Providing a safe environment and quality care for our Veterans is the top priority at the Hines VA Hospital," the statement said. "All Cardiology Peripheral Vascular procedures in 2016 were completed without adverse complications and with good outcomes. Hines VAH has implemented an ongoing Cardiology Quality Improvement Plan that includes validation of the accuracy of the interpretation and technical quality of echocardiography studies, and ensures that all echocardiography technicians have the opportunity for continuing education and training."
Recently sworn-in VA Secretary David Shulkin has vowed to improve patient access to quality VA health care. "I think that we have a system that is doing terrific things with very dedicated people, but we all know we have a lot of work to do and that's what I plan to do as secretary," Shulkin said in February.
Nee is not convinced, and is disappointed no one from the Trump administration or transition team has met with her regarding her allegations.
"You can't have a system that is supposed to take care of patients, and have a system that never takes account for its own mistakes," said Nee.