SACRAMENTO — State lawmakers grilled University of California President Janet Napolitano on Tuesday, saying they found a state audit “extremely troubling,” and questioned whether there is enough oversight of the president’s office.

Lawmakers said they were shocked by the audit released last week, which found UC has a $175 million reserve that no one seemed to be aware of, including the Board of Regents that oversees the university system. But many lawmakers said what disturbed them the most was the state auditor’s contention that the president’s office interfered with and delayed their efforts. For that, Napolitano defended her office, but said she was sorry its actions were perceived as obstruction.

“I deeply believe the trust that has existed between the Legislature and UC has been eroded and that much more transparency is needed,” said Assemblyman Jose Medina, D-Riverside, chairman of the Assembly Higher Education Committee, one of three committees holding the joint hearing on the audit at the state Capitol on Tuesday.

The hearing lasted 4½ hours, with Napolitano leaving visibly exhausted after her two-plus hours of testimony.

“To say this is a black eye on the UC is an understatement,” Medina added.

Among the audit’s findings were that the president’s office hid $175 million in an undisclosed reserve of restricted and discretionary funds as of June 2016. Included in that was $32 million that could have been spent on students, with the audit recommending that those funds be returned to campuses.

The disclosure of that money comes as UC will raise annual student charges beginning next summer by $336, or nearly 3 percent, to $12,630. That includes tuition and a student services fee, which are expected to raise $143 million next year for the UC system.

The undisclosed money accumulated after the president’s office continually overestimated how much it needed to run the 10-campus system, then spent less than budgeted, according to the audit. Auditors said that during 2012 to 2016, the president’s office asked for additional funding using the inflated budgets instead of basing its requests on what was actually spent. That allowed the office to amass a secret reserve that was spent on things like communications and brand management ($4.7 million), the president’s residence ($862,000) and nonresident recruiting ($1.8 million).

State Auditor Elaine Howle said Tuesday that UC’s budget practices were surprisingly weak and ineffective and left regents in the dark on how money was being spent. Howle said the president’s office itself was unaware of just how much it had in reserves because it was kept in various accounts.

Assemblywoman Shirley Weber, D-San Diego, said the auditor’s findings reflect poorly on the regents. Monica Lozano, chairwoman of the Board of Regents, steadfastly defended Napolitano and her office, but said Tuesday that regents would step up oversight.

In the audit, Howle recommended that the Legislature begin overseeing the president’s office budget rather than have the Board of Regents oversee it by having the state directly fund the office. Currently, the president’s office gets its money from the 10 campuses.

Tuesday’s hearing offered no clear direction on whether lawmakers would push for that oversight.

Lawmakers, however, were sharp with their words.

“There does not appear to be in the audit — from my reading of it — any really intended criminal activity,” Weber said. “But, there does appear to be a sense of arrogance and resistance.”

Six Assembly Republicans sent a letter Tuesday to Assembly leadership requesting a subpoena to force UC to produce financial records to “gauge whether or not criminal activity has taken place.”

Auditors sent surveys to each of the 10 campuses to determine if there were any areas in which there was administrative bloat. Howle said those survey responses were intercepted by the president’s office and answers that were once negative were changed to be more positive.

Napolitano said campuses reached out to the president’s office with questions about the surveys. She apologized twice for the impression that the president’s office intentionally interfered with the surveys, which specifically were labeled with warnings saying not to share them with anyone outside of each campus.

“I discussed with chancellors that they should be aware of the surveys and be sure that the responses were accurate and reflect the perspective of campus leadership,” Napolitano said. “While we believe we did things appropriately, it is clear in retrospect we could have handled this better ... I am sorry we did it this way because it created the wrong impression.”

Napolitano denied that her office kept a slush fund, instead saying $38 million was set aside for unexpected expenses, like cybersecurity threat response and support for undocumented students.

The audit also found salaries in the president’s office are “significantly higher” than those of comparable state employees and that executives receive generous benefits, such as a supplemental retirement plan and bonuses.

For example, the UC office of the president’s Chief Financial Officer Nathan Brostrom has a base salary of $424,360. By comparison, Michael Cohen, who is the director of the Department of Finance and oversees the state’s budget, earns $188,451.

“We probably have some of the highest paid people in administration and I would assume they can tell us — I would hope at any moment — what our funds look like; what our balance is,” Weber said.

Melody Gutierrez is a San Francisco Chronicle staff writer. Email: mgutierrez@sfchronicle.com. Twitter: @MelodyGutierrez