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Campus protesters had repeatedly called for the president of the University of Rochester to resign, and on Thursday he did. Credit Rachel Jerome Ferraro for The New York Times

The president of the University of Rochester stepped down on Thursday, just hours before an outside investigation cleared him and his administration of charges that they had covered up sexual harassment by a prominent professor and punished those who spoke out against him.

The president, Joel Seligman, who had been fending off calls for his resignation since the harassment allegations became public in August, announced his decision in an email to the university. The move was made all the more extraordinary by the investigators’ report, which discredited many of the claims against the university and found no legal wrongdoing by Rochester’s leadership.

In fact, the 200-page report said that while the accused professor, Dr. T. Florian Jaeger, had at times acted inappropriately and offensively, and while administrators had missed opportunities to address complainants’ concerns, Dr. Jaeger’s behavior ultimately did not violate university policy at the time. Several of the claims against him, the report said, had been “embellished,” “distorted” or “unduly sensationalized” in an attempt to “demonize” him.

School administrators had examined the complainants’ accusations in good faith and in compliance with university policy and federal law, the investigators wrote, and had not retaliated against faculty members for speaking out.

“I made this decision before I knew what was in the report,” Mr. Seligman wrote in an email to The New York Times. “This was purely my decision. I was not asked by the board to leave, but after a month or so of reflection I came to believe that the best interest of the university required a fresh start under a new leader.”

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The allegations against Dr. Jaeger, a professor in the Department of Brain and Cognitive Sciences, became public in August, after a group of seven current and former professors and one graduate student jointly filed a complaint against the university with the Equal Employment Opportunity Commission. The complaint, and a federal lawsuit filed in December, said Dr. Jaeger had for years harassed and intimidated students and colleagues, and that administrators had punished professors who reported his behavior.

In September, after weeks of student protests and demands that administrators resign, the university’s board of trustees announced that it had placed Dr. Jaeger on leave. It also hired Mary Jo White, a former chairwoman of the Securities and Exchange Commission and former United States attorney for the Southern District of New York, to reinvestigate the claims in the complaint.

Administrators said Ms. White’s investigation, which was overseen by the university’s board of trustees, would provide an impartial assessment of both the accusations against Dr. Jaeger and the school’s harassment policies as a whole.

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Dr. T. Florian Jaeger, a professor in the Brain and Cognitive Sciences department, had been accused of sexual harassment by a number of students. Credit University of Rochester

But the professors who had filed the federal complaint questioned Ms. White’s independence. None of the original complainants agreed to be interviewed by her, citing concerns about bias and their ongoing suit against the university.

Ms. White defended the integrity of her investigation, adding that although she did not speak directly to the original complainants, she reviewed statements and correspondence they had previously provided to university officials.

“People feel, as they should, very strongly about these issues,” Ms. White said in an interview. “It’s just really important to distinguish between allegations and proof.”

The fallout from the complaint has engulfed the prestigious brain science department, which has been ranked as high as fourth in the nation for graduate studies. Four tenured professors who signed on to the complaint have left or plan to leave Rochester; cognitive science professors at other universities said the uproar had dimmed the department’s stature; and more than 450 professors at other universities signed an open letter promising not to encourage their students to enroll or work at the University of Rochester until the administration took action.

The controversy has taken a personal toll, too, with both accusers and defenders of Dr. Jaeger citing ugly attacks and broken friendships.

In the months since the complaint was first filed, widespread revelations of sexual abuse by powerful men have exploded.

The national reckoning has added urgency and national attention to what began as a local, departmental dispute. In December, two of the complainants were included in Time magazine’s list of “silence breakers” — women who spoke out against sexual harassment — honored as the publication’s person of the year.

Ms. White said the report was not a repudiation of the present moment and she did not believe her findings would have a chilling effect on other women, noting that the report had credited the accounts of several women who said Dr. Jaeger had made them uncomfortable.

She also noted that the university had tightened several of its policies since the incidents in question, introducing a rule last year that bars professors from having academic authority over students with whom they have had an intimate relationship. The report recommended that the university go one step further and ban all romantic relationships between students and faculty members in the same department.

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