SAN JOSE — A San Jose State professor found to have sexually harassed a student last year remained the head of his department for nearly five months after the campus investigation concluded, stepping down just days before the end of the academic year, an investigation by this news organization has found.

The case involving Professor Lewis Aptekar raises questions about the campus’s response to a problem that has plagued UC Berkeley and other universities in the past year — and has prompted the campus’s new president, Mary Papazian, to take a hard look.

“I think we can agree that there are things we can learn from the way it was handled,” Papazian told the Bay Area News Group. “We want to get it right. We are looking at it carefully and I’m confident that we’ll do what’s right before this is done.”

Late last week, after receiving questions from this news organization, the campus placed Aptekar on paid leave, according to a source familiar with the case.

Aptekar, who taught in the College of Education’s counselor education department, was accused of repeatedly asking the student during class if she was single and of making comments about wanting to date her. He declined to speak with this news organization directly, but his attorney, Elisa Stewart, said his comments were made in the context of class discussions about romantic relationships. In a counseling class, she said, it’s essential for students to discuss their relationships with family members and romantic partners. When a student remarked that “everyone leaves” her, Stewart said, Aptekar’s response — that he would never leave her — was meant to be supportive.

“From his perspective, he’s being supportive and encouraging, and it’s being construed as sexual impropriety,” the attorney said.

The investigation, however, concluded that the professor’s methods were not appropriate for the classroom, according to documents obtained by this news organization. “(Aptekar) is couching his questioning as educational inquiry, but he is inappropriately using this method to probe for more personal information than (can) possibly be related to an academic program …” the report said.

Instead of removing Aptekar immediately from his post as chairman, a position that extended his reach and influence in the small department, SJSU administrators left the professor at the helm while he also continued to teach and supervise graduate students preparing to be school counselors. After a 10-day suspension last spring, he resumed his duties, but he is not on the current class schedule. Aptekar received $188,890 in pay and benefits in 2015, including total pay of $142,100, according to a Transparent California database.

In 2014, Associate Dean David Bruck filed a complaint against Aptekar on behalf of two other students who came forward with concerns about the professor’s behavior. But it appears that report was not taken into account — or even acknowledged by university administrators — in the 2015 investigation.

Documents show the College of Education’s dean, Elaine Chin, told the investigator probing the 2015 allegations that no one had previously “made any formal or informal complaints” against Aptekar.

Asked whether she had not known about the report filed by Bruck the previous year, Chin referred this newspaper to a campus spokeswoman who said she could not comment.

The students behind the first complaint did not wish to be named for fear of the repercussions, making the claim difficult for the campus to investigate, said Bruck, associate dean of graduate studies for San Jose State. Still, he said, he didn’t understand why the information wouldn’t have been shared with top officials — or considered in the campus response to the second complaint.

“My own opinion is that with three students complaining about sexual harassment against an individual,” Bruck said, “an individual should not remain in the position to be able to repeat that behavior.”

Some familiar with the case say they felt the campus’s response was lacking. For the student, the prospect of running into the professor who knew she had accused him of harassment — and also had been her adviser — created an especially stressful situation, said Dolores Mena, a professor of counselor education, who knew all three students and was aware of their complaints.

“It’s my belief that faculty should protect student rights and provide a safe learning environment,” Mena said. “After seeing the student’s reaction and her anxiety and stress, I was surprised the university took so long to handle this case, considering they had found in favor of the student.”

In the past year, sexual harassment on college campuses has been in the spotlight. A series of scandals at UC Berkeley revealed what was widely felt to be a pattern of light consequences for prominent faculty members and administrators who harassed students or other employees — a track record that appeared to cost the chancellor and his provost their jobs. Both stepped down this year.

At San Jose State, one graduate student said she was not suprised by how the case was handled. Diana Crumedy said in 2012 she complained that another professor had made sexual advances toward her, but “the campus did absolutely nothing to discipline him when I brought it to their attention.” She said she did not believe her complaint was formally investigated by the campus’s Title IX office.

To avoid running into the professor, she said she memorized his schedule.

“I’m sure I’m not the only one,” Crumedy said.

Counselor Education Professor Jason Laker said he advised the student who reported Aptekar after she requested some guidance. Laker said he feels the campus “owes the community an explanation … and immediate reforms to prevent this from happening again.”

“As someone who has worked for 25 years to reduce sexual harassment and gender violence, I feel strongly that professors found responsible for harassing students should not be in the classroom or alone with them,” Laker said. “It’s also frustrating to be conducting research to address these problems while someone down the hall is apparently contributing to them.”

Follow Katy Murphy at Twitter.com/katymurphy.