WASHINGTON (Reuters) - The U.S. Secret Service has put a senior supervisor on leave and suspended his security clearance after a female employee accused him of assaulting her after work at the agency's headquarters last week, the Washington Post said on Wednesday.

The District of Columbia police sex-crimes division and a U.S. government inspector general are investigating the woman's allegation that Xavier Morales of the security clearance division grabbed her on the night of March 31 after they came back from a party at a downtown Washington restaurant, the newspaper said, citing two law enforcement officials with knowledge of the investigation.

Through an agency spokesman, Morales declined to comment, and he did not respond to requests for comment left on his phone, the Post said.

The Secret Service confirmed in an email that an incident had been reported to agency investigators last Thursday and that a supervisor had been placed on administrative leave and the employee's security clearance suspended. The statement did not name the individual or provide any further details.

The case will be investigated by the Department of Homeland Security, Office of the Inspector General, the statement said.

"These allegations as reported are very disturbing. Any threats or violence that endangers our employees in the workplace is unacceptable and will not be tolerated," Secret Service Director Joseph Clancy said in the statement.

The agency that protects the president and his family has suffered a series of scandals in recent years.

It was criticized as being too insular by an independent panel appointed after a man with a knife scaled the White House fence and ran inside the mansion last year.

That incident prompted former Director Julia Pierson to resign. She had been director for two years, named to the top job after agents were accused of hiring prostitutes during a 2012 trip to Colombia.

(Reporting by Eric Walsh and Curtis Skinner; Editing by Louise Ireland)