Over the past three years, UC Berkeley has spent more than $1 million sprucing up the official home of Chancellor Nicholas Dirks, school records show.

Some of the work on the 105-year-old University House, on the west side of campus, began in July 2013 to prepare it for the arrival of the then-newly hired Dirks and his wife, associate history Professor Janaki Bakhle. The $247,000 job — which was approved by then-University of California President Mark Yudof — included a $147,000 renovation of the upstairs kitchen, plus $100,000 for painting throughout the house, refinishing the floors in several rooms and replacing worn window coverings in the residence area with roller shades.

A year later, the university spent $14,752 for more floor work on the lower level of the house, according to records furnished to us by the UC Berkeley real estate division.

Then, in early 2015, the school spent $76,886 to redo a downstairs bathroom used mainly during public events. Leaking plumbing fixtures had caused extensive rot and other damage, officials said.

In a separate purchase not handled by the real estate division, Bakhle swapped nine Persian rugs for six newer ones. The net cost was at least $90,000.

Estimated total cost for the in-home work: $428,000. Campus officials hasten to add that none of it came out of state or tuition funds. Gift funds were used to pay for all the work done ahead of the chancellor’s arrival, while investment income and other revenue sources paid for the rest.

In addition to all this, the university spent close to $700,000 — 2½ times the original budget — to install a security fence after protesters sprayed graffiti on the house. And every year, it provides the chancellor with a $179,000 budget to maintain University House.

News of this spending comes as the university struggles with a $150 million deficit.

University House is the source of another headache for the campus — this one having nothing to do with maintenance.

In 2015, Alice McNeil, who was hired as the house manager and executive assistant to Bakhle shortly after the chancellor arrived, was removed from her post. She was given another assignment outside University House for a while, then was laid off.

Earlier this year, McNeil wrote to UC President Janet Napolitano, alleging she had been pushed out of her job in retaliation for objecting to Dirks and Bakhle having her do long hours of personal chores on UC time — then pushing her to let them avoid reporting the value of those hours to the IRS as their personal income, as required by law.

Those chores, according to McNeil, included picking up groceries for the couple, taking their dogs to the vet and filling out health forms for their teenage son, who was off attending boarding school.

In a follow-up letter to university officials in February, Stephen Henry, McNeil’s lawyer, wrote that “the disagreement (over how many hours were spent doing the couple’s personal business) was made very clear by the chancellor’s wife, who expressed anger over Ms. McNeil’s honesty in preparing the form, and resulted in the removal of Ms. McNeil from University House.”

Napolitano’s office is reviewing the matter. A spokesman there declined to comment.

In an interview, Dirks said he couldn’t comment on a personnel matter but insisted that he and his wife had done everything by the book. He also said McNeil herself had signed all the IRS forms listing her personal work for the couple.

“I paid taxes on it, and there is no issue there,” Dirks said.

As for the fix-up, Dirks said University House is used for 200 to 300 receptions, dinners and other public events a year, and that the only work he and Bakhle had requested was downstairs to replace worn rugs and the main bathroom used by the public.

“It was smelling like excrement and falling apart, and we did ask that it get upgraded so we could have donors go in there,” Dirks said.

As for the new, 7-foot-tall fence and gates outside the house, Dirks said those were security measures recommended by the UC Berkeley Police Department. They will save $350,000 a year, “because we don’t have to have 24/7 security,” he said.

Protected by a fence or not, Dirks has good reason to feel under siege these days. Napolitano was angry over how the campus handled a series of sexual harassment cases, and faculty members are mad about budget cuts that Dirks is making to try to eliminate the deficit — and are quietly talking up a no-confidence vote this fall.

But publicly, at least, Dirks is keeping a stiff upper lip.

“I want to be here for the rest of my career and intend to serve as chancellor as long as I can usefully be of service,” he said.

And how long might that be?

“I’m looking at 10 years — so I got seven more,” he said. “I love this place.”

San Francisco Chronicle columnists Phillip Matier and Andrew Ross appear Sundays, Mondays and Wednesdays. Matier can be seen on the KPIX TV morning and evening news. He can also be heard on KCBS radio Monday through Friday at 7:50 a.m. and 5:50 p.m. Got a tip? Call (415) 777-8815, or email matierandross@sfchronicle.com. Twitter: @matierandross