The Cuomo administration fired a top agency administrator after a state probe substantiated accusations of sexual misconduct, officials revealed Wednesday.

Former Justice Center for the Protection of People with Special Needs boss Jay Kiyonaga engaged in “improper and sexually inappropriate acts” toward female subordinates, state Inspector General Catherine Leahy Scott said in a letter to the Justice Center and the agency where he was most recently employed, the Office for People with Developmental Disabilities.

“The specific acts and pattern of conduct described to my office under oath — ranging from inappropriate sexual comments and comments about employee’s sexual preferences to an unwanted sexual physical contact with an employee — are reprehensible and indefensible,” Leahy said.

The Post first reported on sexual harassment claims against Kiyonaga made by Patricia Gunning, the former special prosecutor/inspector general for the Justice Center, last October.

Gunning said when she complained about his behavior, Kiyonaga retaliated and forced her resignation.

Gunning also contacted Melissa De Rosa, the governor’s top deputy, about the claims following her ouster. De Rosa then referred Gunning’s complaint to the IG’s office to investigate.

One female subordinate testified that Kiyonaga attempted “sexual physical contact” with her during an after-hours social gathering at a bar in 2015, according to the letter. The same witness said he would also talk “about dreams that he had that were of a sexual nature involving staff members.”

Another woman said Kiyonaga once “reached out and kind of caressed my leg to feel the fabric” of her blue pants, which was witnessed by six other staff members.

The same staffer said Kiyonaga once asked her if she knew the definition of “Blumpkin” and she told him she did not.

“It’s when the guy sits on a toilet, gets oral sex and passes feces at the same time,” the witness recalled Kiyonaga saying.

Another female staffer said the married Kiyonaga discussed women’s figures with comments like “nice boobs, nice ass” and suggested he had an open relationship.

Gunning, who on Tuesday filed a sex discrimination complaint against the Justice Center and Kiyonaga with the US Equal Employment Opportunity Commission, said he would regularly and inappropriately “turn the conversation to something sexual” and “pointed out I had a real knack for picking hot girls for my team” and that he had “heard that one person on my staff was bi-sexual and he wanted to know if I knew that and wasn’t it hot.”

Kiyonaga, the number two person at the OPWDD after transferring from the Justice Center, was fired Wednesday.

“OPWDD does not tolerate harassment of any kind. Based on the findings of the Inspector General’s Office, Mr. Kiyonaga has been terminated by our agency,” said OPWDD spokeswoman Jennifer O’Sullivan.

Gunning, through her lawyer, applauded Kiyonaga’s ouster.

“MeToo has finally arrived in New York State government. For years, Ms. Gunning felt ostracized and alone as she suffered sexual discrimination and retaliation at work. Today, she is vindicated. We urge every single victim of Mr. Kiyonaga’s misconduct to come forward and share their experience,” said Ilann Maazel, of Emery Celli Brinckerhoff & Abady.