The Washington Post and other media, citing unnamed law enforcement sources, said Thursday that the action against the official came after a female employee accused him of assaulting her after-hours at the agency's headquarters last week.
Agency spokesman Brian Leary on Wednesday would not provide details of the allegations, but said the Secret Service takes them "extremely seriously."
He said that the incident was first reported to the agency's Office of Professional Responsibility on April 2, after which inspectors conducted corroborative interviews. Director Joseph Clancy was informed the same day, and the employee was placed on leave, he said.
Leary said the Department of Homeland Security's inspector general is now investigating the incident.
"The Secret Service is an agency that demands that our employees conduct themselves with the highest level of integrity," Clancy said in a statement Thursday. "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."
The report is the latest in a string of scandals and controversies surrounding the agency assigned to protect the nation's president and his family. The inspector general is already investigating a March 4 episode in which two high-ranking agency officials are accused of driving into a secure area at the White House without authorization.
The House Oversight Committee is also trying to get to the bottom of allegations that those agents had been drinking when they drove into the area. The agents were accused of nudging a construction barrier with their vehicle as they intruded during an investigation of a suspicious item.
Clancy has faced intense questioning from lawmakers on Capitol Hill about the March incident.
He was named by President
Earlier this year, a small drone aircraft was able to land on the White House lawn, raising additional concerns over security measures.
And in 2012, there was a scandal involving personal misconduct by Secret Service agents traveling in Cartagena, Colombia, before an Obama visit.
Staff writers Kurtis Lee and Ryan Parker contributed to this article.