Felix G. Arroyo, the city’s embattled health services chief, was fired from his Cabinet post Thursday, ending a nearly four-week city inquiry into allegations that he sexually harassed a woman he had been supervising.
“Felix Arroyo has been terminated from the City of Boston after a comprehensive internal investigation,’’ said Laura Oggeri, the city’s communications chief. “The city will immediately begin to search for candidates to fill the chief of health and human services position and we hope to announce an appointment soon.”
The termination derailed Arroyo’s rapid rise in city politics. The son of a prominent Boston political figure, the 38-year-old went from union organizer to City Council aide to two-term councilor. He ran for mayor in 2013, parlaying that campaign into the high-ranking post in Mayor Martin J. Walsh’s administration.
Arroyo was dismissed after a woman under his direct supervision filed a complaint last week with the Massachusetts Commission Against Discrimination, alleging that he has repeatedly sexually harassed her since 2015.
According to the complaint, which was obtained by the Globe, the woman said Arroyo “spanked” her buttocks and grabbed her by the back of the neck when he learned she was going to complain to city authorities. Arroyo, through a spokeswoman, has denied the allegations.
The woman also alleged that city authorities told her to report to another department, when she told them of the alleged misconduct.
The allegations triggered a formal inquiry from the city, and, this week, a police investigation. Arroyo was put on paid leave July 28. On Thursday, the mayor said the city had the assistance of an outside counsel in its investigation.
Walsh said the Arroyo case does not indicate a broader problem at City Hall.
“I don’t think we have fundamental issues with people [being] afraid to come forward with any type of . . . sexual harassment [complaint]. I don’t think that is the case here,’’ said Walsh, before the announcement of Arroyo’s dismissal.
He said the city has strict rules and policies against sexual harassment, noting that department heads and Cabinet holders underwent a recent training on the code of conduct.
Arroyo has not responded to inquiries from the Globe but has denounced the allegations as baseless and retaliatory via statements from his spokeswoman, Colette Phillips, a Boston public relations specialist.
“We are disappointed in this decision,’’ Phillips said. “Felix is adamant that these allegations are baseless and retaliatory and will continue to fight to clear his name and is looking forward to fully cooperating with the MCAD.”
The MCAD complaint names the mayor — who is seeking reelection — the City of Boston, Arroyo, and Arroyo’s chief of staff, Ilyitch Nahiely Tabora. The complaint alleges sexual harassment, retaliation on the basis of her sex and gender, and a hostile workplace.
In the document, the woman said she was hired in October 2015 in the mayor’s Office of Health and Human Services and Arroyo was her supervisor.
“Since the beginning of my employment, Mr. Arroyo sexually harassed me,’’ she wrote.
She added that if she said nothing to Arroyo, the conduct continued daily. If she did ask him to stop speaking “inappropriately and touching’’ her, she said, the behavior stopped and most communications ceased for about three months.
Arroyo resumed the inappropriate behavior on July 24, the woman said, and she decided she could no longer tolerate it. She contacted the city’s human resources department to set up a meeting to discuss the matter. An official in human resources put the meeting on her calendar, which both Arroyo and Tabora can access, the complaint said.
When Arroyo saw the appointment, he called the woman into his office and said “things like ‘you wouldn’t want to hurt me because you wouldn’t want me to hurt you, right?’ ” the document said.
He also said: “You wouldn’t want me to make me look bad, because you wouldn’t want me to make you look bad right?’’ the woman alleges.
She said in the complaint that when she got up to leave his office, Arroyo stood “uncomfortably close to her,” grabbed the back of her neck, and squeezed it very hard.
She met with a human resources official July 25 and the city’s chief of staff, Daniel Koh, the following day. On July 27, she sent Koh an e-mail recounting what Koh told her in their meeting about Arroyo, according to the e-mail she provided to the Globe. “You also asked me to immediately contact you and HR if Felix Arroyo threatens me again or if I felt unsafe in the workplace,’’ the woman wrote to Koh.
On July 28, Arroyo was suspended.
The woman said that the city’s human resources department informed her on or about July 28 that she should report to another department the following week and that she would no longer be in the health services department, according to the complaint.
The woman said she considered the move a demotion and would not have occurred without the mayor’s approval.
The city said the woman asked to move, and the mayor went further, saying the transfer was for the woman’s safety.
The Globe generally does not name victims or alleged victims in certain types of cases.
Arroyo was Walsh’s first appointment to his Cabinet after taking office in January 2014. He oversaw seven departments that serve the city’s most vulnerable populations, including Veterans Affairs and the Public Health Commission.
He had many supporters in the building, but some saw him as a divisive figure.
The controversy has drawn a rebuke from Councilor Tito Jackson, who is running for mayor. Jackson, noting that two of Walsh’s top aides face federal extortion charges, said the Arroyo episode is another indication of turmoil in City Hall. Both Walsh aides have pleaded not guilty.
Jackson scolded the administration for not protecting “the well-being of a city employee.’’Valencia of the Globe staff contributed to this report. Irons can be reached at firstname.lastname@example.org.