The perimeter fence along Pennsylvania Avenue outside the White House is seen in Washington. (Carolyn Kaster/AP)

The Secret Service has put a senior supervisor on leave and suspended his security clearance after a female employee accused him of assaulting her after-hours at agency headquarters last week, the agency said Wednesday.

The D.C. police’s sex-crimes unit and a government inspector general are investigating the female agent’s allegation that Xavier Morales, a manager in the security clearance division, made unwanted sexual advances and grabbed her on the night of March 31 after they returned to the office from a party at a downtown restaurant, according to two law enforcement officials with knowledge of the probe.

The woman told police and agency investigators that Morales, her boss, told her during the party at Capitol City Brewing Company that he was in love with her and would like to have sex with her, according to two people briefed on her statements. In the office later, she alleged, Morales tried to kiss her and grabbed her arms when she resisted, according to the two people briefed on her complaint. The woman alleged that the two scuffled until Morales relented.

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

Late last week, the Secret Service took the unusual step of placing Morales on indefinite administrative leave and adding his name to an internal “do not admit” list prohibiting entry to the office, a Secret Service official said. The Secret Service also took away his gun and badge after agency investigators launched a preliminary review of the complaint and conducted “subsequent corroborative interviews” Thursday afternoon, said agency spokesman Brian Leary.

“The Secret Service is an agency that demands that our employees conduct themselves with the highest level of integrity. These allegations as reported are very disturbing,” Director Joseph P. Clancy said in a statement to The Washington Post. “Any threats or violence that endangers our employees in the workplace is unacceptable and will not be tolerated.”

The inquiry marks the second time in a month that the Secret Service has dealt with alleged staff misconduct after a work-related social event. The Obama administration is looking into a March 4 incident in which two senior agents, returning from a retirement party at a downtown bar, drove an agency car into an active White House bomb threat investigation.

Morales, 48, was among the first group of officials Clancy promoted when he took over as acting director in October after a string of missteps that prompted lawmakers and administration officials to demand fresh leadership and internal reforms.

The March 31 party was held to celebrate Morales’s new assignment as head of the Secret Service’s field office in Louisville — a post that is considered an agency steppingstone. He had been scheduled to report for duty there this week.

The female agent first raised her complaint Thursday with officials in the Secret Service’s internal investigations division.

Clancy was briefed on the allegations later that day, Leary said. Because Morales is a senior supervisor with a GS-15 rank, Clancy asked his investigators to immediately refer the matter to the Department of Homeland Security’s inspector general that day. The criminal nature of the allegations prompted the inspector general’s office to contact D.C. police, according to two people familiar with the police and IG investigations.

D.C. police detectives then interviewed the female agent and the manager on duty that night at Capitol City Brewing Company, according to law enforcement officials with knowledge of the probe. The restaurant manager, who asked not to be identified, told The Post that he had been interviewed by police, but he declined to discuss details.

Police spokeswoman Gwendolyn Crump declined to comment.

The security clearance division Morales helped oversee is responsible for determining when agents, through misconduct or other action, have jeopardized their security clearances and should lose their jobs. It also helps vet Secret Service job applicants for potential security issues.

Last year, Morales was president of the Hispanic American Police Command Officers Association, a national law enforcement group that has had several prominent Secret Service agents as leading members.

Morales is married to a longtime special agent who was recently promoted to be a deputy assistant director over government affairs in the agency’s headquarters.

Peter Hermann and Alice Crites contributed to this report.