SANTA CLARA — After a four-month investigation into Levi’s Stadium finances, the Santa Clara County Civil Grand Jury is recommending that the city immediately order an independent audit to determine whether taxpayer dollars were spent on the stadium.

The 13-page report released Monday caps a volatile year for Santa Clara which saw the sudden resignation of one mayor and accusations of backroom dealings from the next. The grand jury launched the probe into the stadium’s finances after receiving a complaint that public funds were being used to support the multimillion-dollar stadium — a violation of the 2010 voter-approved Measure J, which promised Santa Clara residents that no general fund dollars would pay for the venue’s operations.

“It is unclear whether unreimbursed city general funds are used for stadium operations and maintenance in violation of Measure J,” the jurors wrote.

When city employees, including police and fire officials, set up NFL events or provide security during games, they’re required to report those hours separately on their time sheets so the city can bill the San Francisco 49ers. But there’s no way to determine if an employee fails to accurately report hours worked for stadium events — whether deliberate or accidental.

The audit, which was already requested by Mayor Lisa Gillmor, should outline how city employees get reimbursed for time spent on stadium business, the report said.

Gillmor, who was appointed mayor in February after former Mayor Jamie Matthews suddenly quit, has long suspected the city is violating Measure J and accused officials of engaging in backroom deals. Gillmor went public with her suspicions last month after nearly a dozen employees — including police officers — privately told her they worked during Niners games or non-NFL events at the stadium and the hours were paid with general fund dollars without reimbursement.

The civil grand jury interviewed 11 people and reported many employees said they “were told by superiors to improperly charge Stadium activities to the city.”

But, the jurors concluded, there was no way to corroborate this information. When asked how the general fund is protected, many city employees consistently replied, “I don’t know,” the report said. The jury said an audit will shed light on this process.

“What disturbs me is they were told this was happening, and the audit is more important than ever now,” Gillmor said in an interview Monday. “The grand jury made it clear that we have to make major changes to fulfill our promise to the voters and protect our tax dollars. I vow that we are going to fix this.”

Gillmor plans to ask the City Council to extend the audit’s time frame to when Measure J passed in 2010 — one of the jury’s recommendations — instead of April 2014 when the first NFL season in the new stadium kicked off. She’ll also ask the city to establish a whistle-blower protection program and wants the city manager and city attorney to report what steps are being taken to comply with Measure J.

Acting City Manager Rajeev Batra is not surprised by the report’s findings. He said jurors pinpointed issues that the city is already addressing. On Tuesday, he plans to recommend a firm to conduct the audit and will draft a policy to outline how employees should be reimbursed for hours worked on stadium events.

But Batra could not say why some of his employees said their bosses told them to misreport hours.

“None of my employees have come to me saying that,” Batra said. “I have no idea who said what. They should come and report it.” And in a suburban city plagued by years of strife among its elected leaders, it didn’t take long for the civil grand jury report to turn political.

Patrick Nikolai, former president of the Santa Clara Police Officers’ Association, believes the audit will reveal “several errors” and expenses that were not properly tracked, in violation of Measure J. The longtime sergeant took a shot at police Chief Mike Sellers who he’s challenging on the November ballot.

“Therefore, I call on Chief Sellers to come clean with the public and taxpayers,” Nikolai said. “He should fully cooperate with an audit and allow all officers to come forward with information to uncover the truth wherever it may lead.”

Sellers could not immediately be reached.

The Niners pay $170,000 for public safety costs per game, according to the team’s lease. When costs exceed that amount, the 49ers pay the difference upfront but get reimbursed by the Stadium Authority later. The base rate grows 4 percent a year, but public safety costs have exceeded that amount every year. The city’s fire and police chiefs decide how many people to assign to each game.

But since public safety costs have exceeded the threshold every year since Levi’s Stadium opened, the jurors recommended invoking an option in the team’s lease that allows the city to renegotiate public safety costs.

The jurors also called for reassigning the role of city finance Director Gary Ameling as the Stadium Authority’s treasurer and auditor to avoid the appearance of any “conflict of interest.”

The Stadium Authority, which includes the mayor and six City Council members, was formed to oversee the construction of Levi’s Stadium, to serve as its landlord and oversee other business.

Batra, the acting city manager, supports that recommendation, agreeing that having Ameling in both roles can be construed as a conflict. The city has 90 days to respond to the civil grand jury report’s recommendations.

Contact Ramona Giwargis at 408-920-5705. Follow her at Twitter.com/ramonagiwargis.