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A Veterans Affairs audit of its troubled hospitals and clinics has identified 100,000 veterans facing long waits for health care, and clerks across the system report having been instructed to falsify dates in scheduling records.

The findings, reported by the VA on Monday, indicate widespread confusion across the system charged with caring for the nation’s veterans.

“We must work together to fix the unacceptable, systemic problems in accessing VA healthcare,” Sloan Gibson, the department’s acting secretary, said in a statement.

In the audit, which covered more than 700 VA facilities, 13 percent of scheduling staff reported that they had been instructed by supervisors or others to enter a date in the appointment books different from what the veteran had requested.

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The audit identified more than 57,000 veterans across the country who are facing a wait of three months or more for care at Veterans Affairs hospitals and clinics.

The VA said that it planned to scrap a two-week goal for scheduling appointments because of “growing demand for services and lack of planning for resource requirements.”

The audit also found that almost 64,000 veterans have asked for an appointment at the VA over the past decade but have not been seen.

The VA serves almost 9 million veterans each year. It has roughly 6 million appointments on the books across more than 1,700 facilities.

A former clinic director at the VA hospital in Phoenix charged earlier this year that as many as 40 veterans died awaiting treatment there. An internal VA report last month found that more than 1,500 veterans at the Phoenix facility had been kept off an official waiting list.

It also found that scheduling manipulation was “systemic” inside the VA and dated at least to 2005. VA Secretary Eric Shinseki resigned two days later.

Federal investigators are also looking into allegations that as many as 37 whistleblowers inside the VA were retaliated against, including one VA worker who claimed to have been suspended after reporting improper scheduling procedures.

Twenty-one senators, from both parties, on Friday urged the Justice Department to investigate criminal wrongdoing inside the VA.

The letter said that evidence of criminal wrongdoing was quickly outpacing the VA’s own ability to investigate it.

— Kelly O’Donnell and Erin McClam