An additional 64,000 who enrolled for VA health care over the past decade have never been seen by a doctor, according to the audit.
The audit is the first nationwide look at the VA network in the uproar that began with reports two months ago of patients dying while awaiting appointments and of cover-ups at a VA centre in Arizona.
Examining 731 VA hospitals and large outpatient clinics, the audit found long wait times across the country for patients seeking their first appointments with both primary care doctors and specialists.
It is also a headache for President Barack Obama who had to accept the resignation of the head of the department, Eric Shinseki, on May 30 and is actively seeking someone to replace him after the leading candidate pulled out, citing the prospect of a bitter confirmation hearing.
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Shinseki, a former general, took the blame for what he decried as a "lack of integrity" in the sprawling system providing health care to US military veterans.
The audit said a 14-day target for waiting times was "not attainable," given growing demand for VA services and poor planning.
The audit said 13 per cent of VA schedulers reported getting instructions from supervisors or others to falsify appointment dates in order to meet on-time performance goals.
Acting VA Secretary Sloan Gibson said the audit showed "systemic problems" that demand immediate action.
VA officials have contacted 50,000 veterans across the country to get them off waiting lists and into clinics, Gibson said, and are in the process of contacting an additional 40,000 veterans.