ALBANY — A high-ranking state official who had been the target of workplace complaints filed by female employees dating back years was fired Wednesday by the administration of Gov. Andrew M. Cuomo.

James "Jay" Kiyonaga, second-in-command at the Office for People with Developmental Disabilities, was terminated from his position a day after a former attorney at the state's Justice Center for the Protection of People with Special Needs filed a discrimination complaint accusing Cuomo's administration of covering for Kiyonaga, whom she said had sexually harassed and mistreated her when he was deputy director of that agency.

A letter outlining the findings of an investigation by the office of state Inspector General Catherine Leahy Scott was sent Wednesday to Denise Miranda, executive director of the Justice Center.

"My investigation, which involved numerous witnesses who testified under oath, revealed Kiyonaga's history of improper and sexually inappropriate acts towards and comments to fellow staff members and subordinates at the Justice Center," Leahy Scott wrote. "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."

The Times Union had reported earlier this month that Kiyonaga has been the subject of complaints filed by women at various state agencies where he has worked since 2002, including the Justice Center, the Budget Division and the Division of Criminal Justice Services.

The EEOC complaint filed this week by Patricia Gunning, a former high-level attorney at the Justice Center, cited a "complete failure of the governor's office and the state to deal with this serial sexual harasser and discriminator ..."

"By September 2017, Mr. Kiyonaga's 15 years in state employ had a consistent pattern," the complaint states. "He fostered a boys' club atmosphere in the agencies where he worked. He favored women he found attractive. He retaliated against women who complained."

Gunning's complaint alleged Kiyonaga engaged in repeated sexual harassment, favored or promoted women who "were a willing recipient of his sexual advances," and "distorted Justice Center policy to accommodate his romantic liaison."

Gunning said the Justice Center's general counsel told her that a report on Kiyonaga's conduct was going to be kept on file in their office, but would not be made part of his personnel file — the same way that DCJS handled a similar matter involving Kiyonaga in 2012.

Leahy Scott's investigation confirmed that a Justice Center attorney who headed an investigation of his conduct told him to be "mindful" of how he speaks to colleagues and to be "careful of his staff interactions."

"During my investigation, a number of Justice Center employees testified to my office of other inappropriate acts by Kiyonaga in the workplace and at off-site social gatherings with staff members, including sexual comments to and about female employees and unwanted advances towards female staff members," Leahy Scott wrote in her four-page letter.

A spokeswoman for OPWDD said Kiyonaga was fired due to the findings of the inspector general's office.

"OPWDD does not tolerate harassment of any kind," the statement reads. "Based on the findings of the inspector general’s office, Mr. Kiyonaga has been terminated by our agency."

In 2012, several female employees at DCJS filed a complaint about inappropriate and sexually charged conversations that took place in Kiyonaga's 10th-floor office. Wanda Troche, a former affirmative action officer for the agency, said her investigation was overtaken by the agency's human resources director, Karen Davis, and Mark Bonacquist, the agency's first deputy commissioner.

Troche said she later was told that a sealed envelope apparently documenting something about the case — she wasn't told what it contained — was placed in Kiyonaga's personnel file. The envelope had a notation that it could only be opened by Bonacquist or Davis, she said.

Troche, who retired from the agency in 2015, said the incident was part of a pattern in which the agency's human resources director intervened in matters involving high-level appointees such as Kiyonaga, who transferred to another state agency not long after the incident.

In a federal complaint filed in 2011, Lynn A. Rowe, who worked with Kiyonaga at the Budget Division, said he mocked the way she walked and also made belittling remarks about her hearing. Rowe, according to the complaint, suffers from a serious muscular disease that affects her motor skills, including her ability to walk.

Gunning, a former prosecutor who was appointed by Cuomo as a special prosecutor and inspector general at the Justice Center, filed formal complaints against Kiyonaga that included an accusation he screamed at her in front of colleagues several months after she accused him of manipulating policy decisions to benefit a subordinate who was his romantic interest.

"He repeatedly retaliated against me before he got moved along (to another agency)," Gunning said in a recent interview, adding that she was forced to resign, in part, due to the agency's inaction.

Gunning said she also complained that Kiyonaga had made sexually charged comments about female members of her staff as well as other inappropriate comments related to sex. Again, she said, nothing was done.

Melissa DeRosa, secretary to the governor, referred Gunning's allegations to the inspector general's office after Gunning contacted her several months ago. Gunning contacted the governor's office, she said, after Justice Center officials had stated publicly that they investigated the allegations and determined they were unfounded, even though some of the incidents were witnessed by other employees.