When an internal VA audit released this week flagged the Livermore medical facility as a site of potential scheduling irregularities, it raised concerns that the wait-time problems experienced by veterans had spread to the Bay Area.

Dr. Stephen Ezeji-Okoye, the VA Palo Alto Health Care System's deputy chief of staff, said a Livermore Division employee claimed to have been "instructed to do something not consistent with VA policy" in scheduling medical appointments for veterans. Ezeji-Okoye said VA investigators who conducted on-site interviews did not specify what exactly was alleged.

"It's speculation at this point, but we have to assume that the employee scheduled something other than what was requested by veterans," Ezeji-Okoye said. "We're encouraged that this doesn't appear to be widespread. But it's concerning that an employee felt they had to schedule an appointment in something other than what the veteran wanted."

Manipulating the appointment process to make patient wait times appear shorter is at the heart of a VA scandal that began with allegations of cooked books at a Phoenix center. The furor already has resulted in the resignation of VA Secretary Eric Shinseki.

Livermore, which is one of 10 sites in the far-flung VA Palo Alto system that treated 67,000 patients last year, was the only Bay Area facility cited as needing further investigation by the audit.

In a statement released Tuesday, VA Palo Alto Director Lisa Freeman said she already has met personally with Livermore's staff "to ensure that there is a common understanding" of scheduling practices.

Ezeji-Okoye added: "At this point we have to find out the full extent of the allegation, attempt to substantiate it and then take the corrective action needed. We're surprised that someone felt that they needed to do something contrary to our policy."

Rep. Eric Swalwell, D-Pleasanton, in a statement, said he was assured last month during a visit to Livermore that the long wait times at other VA facilities were not experienced here in the Bay Area.

"I await the full report and in the meantime will independently reach out to veterans in the East Bay to ensure they are receiving the timely and quality care they were promised and have earned," Swalwell added.

Monday's report found that 57,400 vets nationally have waited more than three months to receive a medical appointment and that an additional 64,000 had requested medical care but had not been seen for an appointment.

The audit also found that 13 percent of VA schedulers had been instructed to enter false information to hide the real length of time veterans waited for appointments. Of the 731 facilities in the VA system, which schedules 6 million appointments, 112 were found to have issues -- including Livermore.

The report drew fresh outrage from critics who said it showed that the deficiencies in prompt medical care are systemic throughout the VA.

Sloan Gibson, the interim secretary, said the VA will spend $300 million to increase the hours of medical staff as well as contract with private clinics to reduce the patient wait times. Also, Gibson said he is eliminating the 14-day scheduling goal for VA appointments. Officials have said that controversial metric is unrealistic with current staffing levels and may have led to hospital administrators altering wait-list data to earn bonuses.

VA Palo Alto was not among the medical centers with the longest wait times, according to the report. The average time to schedule an appointment for new patients is 42 days.

In a recent interview with this newspaper, Freeman said she believed there was no wait-list manipulation occurring in their system. VA Palo Alto has about 350 employees who schedule patient appointments.

Affiliated with the Stanford University School of Medicine and ranking as the VA's second-largest research facility, it is widely considered one of the best in the national system. In satisfaction surveys, Bay Area veterans have given it a 75-percent approval rating for access of care in a timely manner and a 90-percent approval for medical care, a spokesman added.

Follow Mark Emmons at Twitter.com/markedwinemmons.