The Yale School of Medicine forced Dr. Rex L. Mahnensmith to resign. He also lost his job as medical director at the New Haven Dialysis Clinic. CreditChristopher Capozziello for The New York Times 

For the second time in less than a year, the Yale School of Medicine is embroiled in charges of sexual harassment.

A nephrology professor, Dr. Rex L. Mahnensmith, who worked at the university for over 20 years, has been accused of a pattern of sexual harassment while he was medical director of the New Haven Dialysis Clinic, where university physicians treat their patients.

Last year, when the accusations boiled over but were being handled quietly by Yale, the clinic removed him, and Yale forced his resignation. But now, two federal lawsuits have been filed against him in Connecticut, detailing a history of sexual misconduct that stretches back more than a decade.

For Yale, the federal cases are an unpleasant echo of sexual harassment accusations last year involving the former head of cardiology at the school. And they are not the first time that the university has had a complaint about Dr. Mahnensmith, whose lawyer said neither he nor the doctor could talk about pending litigation.

In a separate case a decade ago, not previously made public, a young nephrologist filed a formal university complaint of sexual misconduct against Dr. Mahnensmith. The complaint was resolved when he was ordered to attend sensitivity training — an outcome that faculty members familiar with the case say was at the time considered a major victory for women’s rights at Yale.

These days, though, the stakes could be higher as universities are increasingly being held accountable for sexual misconduct, whether by employees or by students.

Nancy Gertner, a retired federal judge who teaches at Harvard Law School, said universities that might have looked the other way when confronted with such accusations were “all of a sudden finding that there’s a realistic risk of losing funding if they don’t take complaints seriously.”

The federal court cases were filed on behalf of seven present and former employees of the dialysis center, including nurses, a social worker and a dietitian. The center is run by DaVita, a private company based in Denver. The center is a defendant in the cases, along with Yale and the doctor.

In 2002, the complaints say, Dr. Mahnensmith, now 63, pressed his erect penis against the back of one of the plaintiffs, a social worker, while she was seated on a stool. She reported the episode to her supervisor, who told her that this was the “culture of the clinic” and that she should try to avoid Dr. Mahnensmith. Similarly, the complaints say, in July 2013, the doctor went into a patient’s room where one of the nurse plaintiffs was sitting on a stool, facing away from the door, and pressed his erect penis against her back while “firmly holding and rubbing her shoulders.”

“This has been going on for years,” said Jennifer Zito, the lawyer for six of the plaintiffs. “But staff were just told to try and work around him.”

The woman in the case from a decade ago, whose name was never made public, declined a request to comment on the case last month. But in interviews with five nephrologists who trained or practiced at Yale during Dr. Mahnensmith’s tenure — all of whom spoke on the condition of anonymity to candidly discuss a member of their profession — each cited instances of inappropriate behavior.

A spokesman for Yale declined to discuss either the pending litigation or previous complaints, saying only that the university takes sexual harassment accusations seriously, and is working to improve the climate for women.

DaVita stressed to its staff its “intent to keep Dr. Mahnensmith happy to protect its contracts with Yale,” the complaints say, because “the Yale contracts afforded DaVita both financial gain and status.” To preserve that connection, court papers say, DaVita failed to act when clinic administrators reported Dr. Mahnensmith’s misbehavior.

A DaVita spokesman declined to discuss the case but said it had removed the doctor from practice at the clinic in January 2014.

Yale and DaVita received a draft of the complaint in March 2014, said Ms. Zito, the plaintiffs’ lawyer; Dr. Mahnensmith was forced from the Yale faculty in mid-April. Currently, Dr. Mahnensmith offers medical advice on HealthTap, a virtual medical practice, where he lists his affiliations with Yale Internal Medical Associates and Yale New Haven Hospital. His LinkedIn profile says he started a job at Genesis Healthcare, a nursing home, in September; Genesis did not respond to requests for comment.

After unsuccessful mediation efforts, the lawsuits were filed in February — one on behalf of six plaintiffs, the other on behalf of another plaintiff.

The complaints say that in November 2013, Dr. Mahnensmith went into a conference room with several of the plaintiffs and stood behind one of them “thrusting his pelvis in a sexual manner into the back of her chair rocking it to and fro.” After another of the plaintiffs told him to sit down, the papers say, “Dr Mahnensmith replied with a smirk, ‘I’m not finished yet,’ and continued to sexually gratify himself until announcing to the group that he was finished.”

That same month, the complaints said, Dr. Mahnensmith did the same thing to a nurse in front of two other plaintiffs.

In December 2013, Elizabeth Chiapperino, a DaVita facility manager, contacted a DaVita vice president about the doctor’s conduct, the complaints say. The vice president “trivialized” the matter, according to the court papers, and expressed concern about how the accusations might affect DaVita’s relationship with Yale. Ms. Chiapperino resigned Jan. 3.

The complaints against Dr. Mahnensmith go beyond sexual harassment, accusing him of not following Yale’s or the center’s policies on prescription drugs, but of enticing drug-seeking patients to have dialysis at the center “by prescribing them narcotic pain relievers such as Fentanyl and MS Contin.”

Members of the Yale medical school faculty, who requested anonymity because they had been instructed not to speak to the news media, said it was widely known that Dr. Mahnensmith wrote a great many prescriptions for the painkiller Percocet, unusual in a dialysis practice.

Dr. Stefan Somlo, head of the nephrology department, did not return phone calls.

The dean of the medical school, Dr. Robert J. Alpern, also a nephrologist, has recently come under fire from the faculty for failing to take strong action against sexual harassment.

In the case of the former cardiology chief, Dr. Michael Simons, a young researcher’s complaint was heard, then reheard, by a university commission. The commission twice recommended that Dr. Simons be permanently removed as cardiology chief, and kept from positions of power for five years.

But that confidential recommendation was ignored. Instead, the medical school, with no mention of any wrongdoing, announced that Dr. Simons would step down as cardiology chief for 18 months, then resume the job. Dr. Simons was also allowed to remain head of the Cardiovascular Research Center.

When the dilution of the recommended penalty became known last fall, many faculty members protested, complaining that the dean overlooked inappropriate behavior by faculty members who brought in substantial income. As the publicity grew, Dr. Simons was removed as chief of the research center, and he did not return as chief of cardiology.

Dr. Alpern appointed an Ad Hoc Task Force on Gender Equity, whose report is expected shortly.