The Department of Veterans Affairs (VA) is facing mounting evidence that some of the hospitals it runs have been keeping two sets of books to make it look as if they were reducing waiting times to see a doctor.

More damning, the department is investigating the claims of a whistleblower doctor in Arizona that dozens of patients at one hospital died while they were languishing on a hidden waiting list without ever being given an appointment.

Richard Griffin, the department’s acting inspector general, admitted on Thursday that its review could lead to criminal charges. In the first political casualty of the scandal, Robert Petzel, the department’s undersecretary for heath, resigned on Friday.

If the evidence of mismanagement continues to accumulate, the Obama administration will find itself not in another partisan knife-fight, but under fire from both parties in a Congress where the uniformed military is venerated.

The veterans’ healthcare scandal is, in part, one of the unintended consequences of the wars in Afghanistan in Iraq, which have created “our 9/11 generation who have served with honour in more than a decade of war,” as President Barack Obama described them on Thursday.

More than 970,000 veterans from those wars have filed disability claims, taking the total enrolled in the VA system to 8.57m by the end of 2012.

At the same time, the healthcare system is dealing with the fact that many of the 6m veterans from the Vietnam era are now reaching the age when they start to require a lot of medical services. In 2010, the administration expanded coverage to exposure from Agent Orange, the chemical used during the war in Vietnam, prompting another surge of claimants.

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