UC Berkeley’s top research administrator has resigned from his $400,000-a-year post under protest, amid allegations that he sexually harassed his top assistant, including touching her breasts, kissing her on the neck and declaring he wanted to “molest” her.

Adding to the drama, his accuser, ex-Assistant Vice Chancellor Diane Leite, was herself fired from UC Berkeley three years ago after it was revealed that she was having an affair with a much younger male subordinate, whose salary she had doubled during the 15 months they were together.

UC Berkeley Chancellor Nicholas Dirks announced Vice Chancellor Graham Fleming’s exit in a brief memo to senior staffers last week, saying the research chief had informed him he was stepping down for personal reasons.

Dirks praised the 65-year-old Fleming for helping UC Berkeley attract hundreds of millions of dollars and maintain its position as one of the world’s “elite research universities.” A spokesman for the chancellor said Fleming would leave his post April 20 and that UC would have no further comment.

The resignation follows a complaint that Leite filed last year with UC President Janet Napolitano, whose office concluded that Fleming had “more likely than not” violated the university’s anti-sexual-harassment policies.

Leite, now 50, worked under Fleming until her firing in 2012. Among her allegations:

•In 2009, while on a university business trip, Fleming rubbed Leite’s feet while they were lying on a hotel room bed fully clothed and put his arm around her.

•Fleming touched her breasts during a gathering with colleagues in 2009 at the Cal Faculty Club and said he wanted to “molest” her.

•He kissed the back of her neck in 2011 and sent “affectionate and familiar e-mails” to her over an extended period.

In January, Fleming sent Chancellor Dirks a letter acknowledging that he had “used poor judgment” with Leite on several occasions and that he “sincerely” regretted the actions, “as well as the embarrassment those actions may cause the university.”

“However, I strongly deny that any of my actions toward Ms. Leite were unwelcome or otherwise constitute sex harassment,” Fleming wrote.

Fleming wrote that he had a “close, mutually respectful and somewhat affectionate working relationship” with Leite, but that “it was not at any time either sexual or romantic.”

Leite and her attorney did not return phone calls last week seeking comment.

Napolitano’s office concluded in December that there was enough evidence to take disciplinary action against Fleming, effectively forcing him to step down after six years at the helm of UC Berkeley’s all-important research arm.

Among other things, the investigation by Napolitano’s office found that some of Fleming’s behavior toward Leite indicated a “sexual interest in her” and that her actions demonstrated that some of Fleming’s “behaviors were unwelcome.”

Fleming declined comment to us, but public relations consultant Sam Singer, who is working with Fleming’s lawyer, said the former vice chancellor is being “railroaded.”

In a letter to Dirks dated April 8, Fleming said he was resigning under protest and blasted the UC investigative report as “riddled with inconsistencies, mischaracterization of the facts and distortion of witness statements, as well as the selective omission of relevant information.”

Among other things, Singer says, Fleming categorically denies the most explosive allegation — that he touched Leite’s breasts. Singer also said the “molest” remark was a bad joke, for which Fleming had promptly apologized.

Fleming’s legal and PR team said the vice chancellor had asked that another investigator from Napolitano’s office be appointed to conduct an “independent and unbiased review,” but that the UC president had “summarily rejected’’ the request.

“We followed our normal processes, and we’re confident they were properly conducted,” countered Steve Montiel, press secretary to Napolitano. He declined to comment further.

Fleming’s exit is the latest chapter in a drama that began in 2011 when Leite’s relationship with purchasing manager Jonathan Caniezo, who is 17 years her junior, was detailed in a whistle-blower letter to her university bosses. While the two were together, Caniezo’s annual pay grew from $57,864 in 2008 to $120,000.

UC Berkeley officials concluded that Leite had violated the school’s sexual harassment policies. She was reassigned from her $188,000-a-year job as head of the research office to an adviser’s role that paid $175,000.

After news of the scandal broke in 2012, UC came under sharp attack from both the public and legislators in Sacramento, and campus officials asked Leite to resign. When she refused, Fleming fired her.

According to Singer, Leite had plenty of chances to sound the alarm on Fleming’s alleged behavior before she was fired, but never did. Singer’s take is that Leite “made these false charges against him because he did not protect her job.”

The inquiry by Napolitano’s office, however, reached a different conclusion — one that puts a twist on Leite’s harassment claim. It found that Fleming, smitten with Leite, had used his position to “actively interfere” with UC’s effort to fire her.

As it turns out, Fleming — a tenured chemistry professor who has been at the university for 18 years — won’t be heading for the unemployment office. After taking a year’s sabbatical, he will be allowed to resume teaching — though for considerably less money than he made as a vice chancellor.

As for Leite, she’s now working as a research director at the Joint BioEnergy Institute in Emeryville. It’s a research program that has ties to both UC Berkeley and Lawrence Berkeley National Laboratory — and was founded with Fleming’s help.

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 e-mail matierandross@sfchronicle.com. Twitter: @matierandross