UC Berkeley Vice Chancellor for Research Graham Fleming, whose resignation was announced Thursday, has denied allegations of sexual harassment made by a former campus employee, criticizing the university’s investigation of the allegations.

The UC Office of the President began its investigation of Fleming last year, when former assistant vice chancellor for research enterprise services Diane Leite filed a complaint that Fleming violated university anti-sexual harassment policies by allegedly inappropriately touching her and sending overly affectionate emails.

According to the San Francisco Chronicle, UCOP concluded that Fleming “more likely than not” violated the policies.

A news release from public relations consultant Sam Singer, who works with Fleming’s lawyer, said Fleming denied the charges of harassment made by Leite and resigned under protest, saying UCOP “mishandled” charges made against him in the investigation.

“(UCOP) bungled the investigation,” Singer said. “Fleming’s legal counsel provided ample evidence that the allegations are false.”

According to the release, Fleming’s counsel provided evidence to UCOP that said that the findings were not supported and that the investigation was biased. Fleming’s counsel unsuccessfully sought retraction of the investigation report.

In his resignation letter to Chancellor Nicholas Dirks, Fleming said the investigation violated his right to due process and produced a report “riddled with inconsistencies, mischaracterization of the facts, … distortion of witness statements, as well as the selective omission of relevant information.”

UCOP spokesperson Steve Montiel said that the university followed its normal processes and that it is confident that the processes were properly conducted. He declined to comment further.

According to Singer, Fleming was first made aware of the allegations last year, two years after Leite was fired for allegedly violating university policies after she increased the salary of one of her employees with whom she was having a sexual relationship.

Additionally, Fleming denied UCOP findings that he had a “conflict of interest” during the investigation of Leite in 2012 and had improperly tried to protect her job.

Fleming said he and Leite had a “long-standing and affectionate friendship” for almost 11 years but were not sexually or romantically involved, according to the release.

Fleming served as Lawrence Berkeley National Laboratory’s deputy director from 2005 through 2007 and played a role in bringing the Energy Biosciences Institute to UC Berkeley, the release said.

Leite is currently working at the Joint BioEnergy Institute in Emeryville, a research foundation with ties to the Berkeley lab, as director of research advancement.

According to a letter from Dirks, Fleming resigned for “personal reasons” and will end his term April 20 with plans to return to teach in the department of chemistry.

Pending approval, Chris McKee, a UC Berkeley professor of physics and astronomy, will serve as the interim vice chancellor for research.