After guards at the Marcy Correctional Facility in central New York beat a handcuffed prisoner to death late last year, Gov. Kathy Hochul promised immediate reforms to turn the troubled prison around.

One of her first directives was to install a new leader, Bennie Thorpe, who had recently run another correctional facility and had experience with security operations and rehabilitation programs. Mr. Thorpe, she said, had “expertise and a fresh perspective on what must be done.”

He also had a record of being accused of rape and sexual assault by inmates at one of his former workplaces, records and interviews show.

In lawsuits filed in 2023, two women who had been incarcerated at the Bedford Hills Correctional Facility in Westchester County accused Mr. Thorpe of sexual abuse when he was a captain there.

One said he summoned her to an office, groped her breasts and raped her in December 2018.

Another said he raped her three times in the spring of 2019 in a room near the prison’s medical unit.

Neither of the allegations has been previously reported. Both lawsuits are still pending in the New York State Court of Claims.

Mr. Thorpe did not respond to multiple requests for comment.

A spokesman for the New York State Department of Correction and Community Supervision said that internal investigators reviewed the allegations against Mr. Thorpe in 2018 and 2019 and determined them to be “unsubstantiated.” The spokesman, Thomas Mailey, declined to comment on the lawsuits but said that the department had confidence in the investigators’ findings.

A representative of Ms. Hochul’s office directed questions about Mr. Thorpe’s appointment to the Corrections Department.

It was not clear how Ms. Hochul, a Democrat, had identified Mr. Thorpe for the role or whether the Corrections Department had informed her of the allegations against him. The representative declined to say whether the governor was aware of the pending lawsuits against Mr. Thorpe when she directed that he run Marcy Correctional Facility.

Jennifer Scaife, the executive director of the Correctional Association of New York, a prison oversight agency, said Mr. Thorpe’s promotion was emblematic of larger concerns with the prison system.

“These kinds of abuses of incarcerated people are so pervasive and normalized,” she said, “that someone accused of abuse just six years ago could be elevated to a superintendent position.”

The first woman to accuse Mr. Thorpe, Michelle Spirles, was convicted of manslaughter in Monroe County in 2011 for stabbing her abuser and sentenced to 25 years.

She was sent to Bedford Hills, a state prison for women, and eventually made her way to an honor dorm, which afforded inmates fewer restrictions and more privileges than other areas.

One evening in mid-December 2018, Ms. Spirles was awaiting a security check in her cell when an officer told her to report to another building, her lawsuit said.

It was an unusual order because the other building housed counselors’ offices and disciplinary rooms. Most of its staff members had left for the day, she said.

When she walked in, a far-off voice directed her to move down the hall, where she saw Mr. Thorpe, then a captain, standing with his penis exposed, she said. He fondled her breasts and vagina and raped her, her lawsuit said.

She reported the assault to prison internal investigators, an inmate grievance officer and the Westchester County district attorney’s office, her lawyers said. Afterward, she was locked in her cell for long periods, issued bogus misbehavior reports and slammed into doors as retaliation, she said.

Her lawsuit accuses the state of failing to protect her. It also says that the state failed to “discipline, remove, suspend, terminate or transfer” Mr. Thorpe after the assault.

After serving 12 years, Ms. Spirles won early release under a law that allows leniency for people whose convictions were related to domestic abuse. But since the alleged sexual assault, she has struggled.

“It changed my whole life,” Ms. Spirles said in an interview, squeezing a stress ball as she spoke. “I don’t know when I will ever be the same. I am trying not to let it destroy me.”

Months after the assault that Ms. Spirles said occurred, another woman, Sedetrice Wright, was also sexually assaulted by Mr. Thorpe, Ms. Wright said in her own lawsuit. Ms. Wright had just entered the prison system on a five-year sentence for assault.

In the lawsuit, she said that Mr. Thorpe assaulted her three times in March and April 2019, raping her and forcing her to perform oral sex.

“This is a public safety issue,” said Ms. Wright’s lawyer, Anna Kull of the firm Levy Konigsberg, “and the state has not taken any proactive or corrective steps.”

Both lawsuits were filed under a law that provides a one-year window for bringing claims over assaults that occurred years earlier.

A lawyer for Ms. Spirles questioned whether the state realized whom it had promoted to run the Marcy Correctional Facility after the beating death of the inmate, Robert Brooks.

“Where are the reforms?” asked the lawyer, Adam Slater of the firm Slater Slater Schulman. “Where are the hearings? Where are the investigations?”