One of the two executives who resigned this week from the University of California president’s office wrote emails directing campuses to reveal and sometimes alter their answers in a confidential state auditor’s survey, which tainted the review and prompted the state to demand an investigation. The other was his boss, who was copied on many of the emails.

Seth Grossman, chief of staff to UC President Janet Napolitano, and Bernie Jones, his deputy, “resigned to pursue other opportunities,” a UC spokeswoman said Wednesday.

As a result of the emails, three of UC’s 10 campuses — Santa Cruz, San Diego and Irvine — changed their survey responses to reflect more favorably on the UC Office of the President, which was being audited by the state. Auditor Elaine Howle, who released the audit results in April, discarded the survey results and said the interference by the president’s office made them useless.

The emails, obtained by The Chronicle, indicate that Napolitano was briefed on the reviews of campus survey responses. And Karen Petrulakis, who was chief deputy general counsel until her departure in July, was also copied on many of the messages between the president’s office and the campuses.

The UC regents hired former state Supreme Court Justice Carlos Moreno in June to conduct an independent investigation into alleged tampering, and the results are pending. Last month, Gov. Jerry Brown signed a bill requiring a $5,000 fine imposed on anyone who interferes with a state audit. That law, prompted by the UC debacle, takes effect Jan. 1.

At the time of the audit last fall, the UC president’s office in Oakland had an annual budget of $686 million and nearly 1,700 employees. Among the audit’s revelations were that the president’s office squirreled away $175 million in reserve funds it didn’t disclose to the public, and that it paid employees “significantly higher” than state workers in comparable jobs.

Angry state lawmakers grilled Napolitano in May, prompting an apology and promises from the president and then-regents Chairwoman Monica Lozano that UC would implement each fix recommended by the auditor. Brown is withholding $50 million in state funding from the university until those are done.

As part of the audit process, Howle surveyed the campuses to learn which services from the president’s office were useful, and which might be a waste of money. The questionnaires were marked confidential and were not to be shared outside campus.

“Quickly checking to see when we might expect the documents for our review,” Jones wrote to UC Santa Cruz on Nov. 21, 2016.

A day later, Jones followed up: “Our expectation is that we review an updated version of the survey responses before it is resubmitted” to the auditor.

Jones also told UC Santa Cruz to “communicate directly with me, and I can then brief Seth (Grossman) and the President, as needed.”

UC Santa Cruz Chancellor George Blumenthal responded a day later, copying Grossman. “As you will see, I addressed 98% of your concerns,” he wrote, and, in a separate email, referred to “Bernie’s marked up version.”

A comparison of survey answers before and after interference by the president’s office showed that administrators at UC Santa Cruz, UC San Diego and UC Irvine removed criticism of Napolitano’s office or upgraded performance ratings in key areas at the direction of Napolitano’s staff.

Jones, whose last day is Thursday, declined to comment on the audit. He said only that his departure, seven years after arriving in the Bay Area, “fulfills a long-standing commitment to my family to return back East.” He called it a “tough choice to leave UC,” and a “bittersweet transition.”

Nathan Ballard, a spokesman for Grossman, said his involvement in the audit survey process was “very limited.”

“The process of working with the individual campuses to review the survey responses was suggested by the university’s internal audit staff and reviewed and approved by the university’s attorneys,” Ballard said. “The university’s attorneys were directly involved in working with Bernie (Jones) and the campuses’ responses to the surveys.”

UC spokeswoman Dianne Klein said that neither Jones nor Grossman had been forced to leave.

Klein, who is also Napolitano’s spokeswoman, did not respond when asked by text and email about the president’s involvement in the surveys.

At UC Santa Cruz, survey responders initially rated technology help from the president’s office as “poor.” That became “good” after Napolitano’s office intervened. The campus also changed ratings for three services previously judged “fair” to “good.” And they changed their ratings of three other services, including help in identifying top-performing high school students, from “good” to “exceptional.”

UC San Diego’s original survey said administrators were “dissatisfied” with explanations from the president’s office about how it spends the campus fees that keep it afloat. They became “satisfied” after the president’s office reviewed it.

At UC Irvine, survey ratings on questions about the quality of collaboration with the president’s office over campus fees were changed from “OK” to “satisfied,” and others from “satisfied,” to “very satisfied.”

The UC regents will meet in San Francisco on Wednesday and next Thursday. No discussion of the Moreno report is scheduled. The regents will hear an update on UC’s progress implementing other areas of the audit recommendations.

Nanette Asimov is a San Francisco Chronicle staff writer. Email: nasimov@sfchronicle.com Twitter: @NanetteAsimov

Online extras

Here are links to two sets of email exchanges between the UC Office of the President and several campuses regarding review of campus survey responses:

http://www.sfchronicle

.com/file/252/4/2524

-Emails2.pdf

http://www.sfchronicle

.com/file/252/3/2523

-Emails.pdf

Here is a link to all Chronicle’s coverage of the state audit of the UC president’s office:

www.sfchronicle.com/

ucaudit