Also flagged in Pennsylvania for more investigation were an outpatient clinic in Horsham and the VA medical centers in Lebanon, Altoona, Erie and Pittsburgh, plus the one in Wilmington. The only New Jersey site to make the list is the VA New Jersey Health Care System campus in Lyons, Somerset County.
Nationally, the report found that more than 57,400 veterans had been waiting 90 days or longer for new-patient appointments. The audit results stoked new outrage among veterans advocates, calls for a criminal investigation, and a pledge by the VA to change its policies.
Philadelphia VA spokeswoman Jennifer Askey said staff there had been aware of problems with access times for nearly a year and were addressing the issue. She also said staff were monitoring wait times and scheduling practices every day while administrators look to provide more community-based care opportunities for veterans waiting to be seen.
Askey also said the center's director, Daniel Hendee, in May contacted the VA's Office of Inspector General - which is conducting a more focused investigation of about 42 facilities - and requested a review.
At least one Pennsylvania center had been reported to be in that probe, but the inspector general has not released a list.
"Staff members at the Philadelphia VA Medical Center are deeply committed to providing quality care to each and every veteran they are privileged to serve," Askey wrote in an e-mail.
A staff member said the Horsham clinic was a satellite site under the Philadelphia VA and referred comment to officials there.
Monday's findings indicated the depth of a scandal that has been building for months, since reports first surfaced of patients dying while their cases languished on secret waiting lists. The claims led to the resignation of Veterans Affairs Secretary Eric K. Shinseki and the audit of 731 VA sites. About 15 percent of those were flagged Monday for further review.
The audit found widely varying average wait times, most outside the VA's 14-day goal, including 86 days for a specialty care appointment in St. Louis and 40 days for a mental health appointment in Bay Pines, Fla.
Philadelphia's average for a primary care appointment was 43 days. At the Coatesville VA, it was on the lower end, at 17 days.
The report also suggested doctoring or concealing waiting times for veterans was not unusual.
About 8 percent of scheduling staff said they had used alternatives to the official waiting list, in some cases because they were pressured to hide delays, the audit said. It found 13 percent of the scheduling staff indicated they had been told by a supervisor to enter a different date from the one requested, a practice it said can be acceptable in some circumstances.
In at least two clinics, staff believed someone other than a scheduler was routinely changing dates to improve performance, the audit found.
The report urged caution in interpreting the data, as the VA deployed 400 staffers across the country to complete the interviews over five days.
That did not stop legislators from responding harshly, including 19 senators who urged U.S. Attorney General Eric Holder to launch a criminal investigation. "Evidence of secret waiting times, falsification of records, destruction of documents, and other potential criminal wrongdoing has appalled and angered the nation, and imperiled trust and confidence in the Veterans Health Administration," the bipartisan group wrote in a letter released Monday.
The VA said that "where appropriate," it would begin removing senior leaders. It has also eliminated the 14-day appointment goal, a practice that has been tied to staff bonuses.
Acting Veterans Affairs Secretary Sloan Gibson, who replaced Shinseki late last month, ordered the Veterans Health Administration to begin developing a patient satisfaction measuring system to provide real-time, location-by-location data.
"As of today, VA has contacted 50,000 veterans across the country to get them off of wait lists and into clinics," Gibson said in a statement. "Veterans deserve to have full faith in their VA, and they will keep hearing from us until all our veterans receive the care they've earned."
Veterans groups called the results deplorable. Daniel M. Dellinger, national commander of the American Legion, said the number of veterans waiting for service was disgraceful.
"This is not just 'gaming the system.' It's Russian roulette, and veterans are dying because of the bureaucracy," he said in a statement.
In interviews at the Philadelphia VA Monday, six veterans said they had received care when they needed it.
"I have no complaints," said 65-year-old Byron Mosley of Philadelphia, who was there for a follow-up appointment after having a hip replaced in February. "I don't have a problem with this place."
The sentiments echoed those in recent weeks by U.S. Rep. Chaka Fattah, a Philadelphia Democrat whose district includes the Philadelphia medical center and who has defended the care offered there. He has stressed that a review does not prove misconduct.
"I'm not going to be alarmed until I have more facts," Fattah said Monday. "If they couldn't get in because the VA didn't have the expertise and referred them to a private provider in the area, that would be one thing we need to know."
Rep. Mike Fitzpatrick, a Republican from Bucks County, said in a statement he was happy the VA audit was released, but it "does little to comfort the thousands of veterans in my district who seek medical care and benefits from the Philadelphia offices."
Sen. Robert Menendez (D., N.J.) said in a statement that the audit underscored "the critical need for reform" in the VA.
Sen. Robert P. Casey (D., Pa.) said he expected the Philadelphia VA to prove it had acted to correct any problems.
"When the Philly center makes an assertion about having seen a problem and dealing with it, they've got to be able to prove it," he said. "And so we'll see what they put on the table to measure proof that they're really confronting it and fixing it."
Inquirer staff writer Rachel Zamzow contributed to this article.