The envelope arrived Monday, and the agency did not announce to whom the letter was addressed. Further tests are being conducted to confirm the initial results.
Answering pointed questions about new claims of misconduct by his agents, Joseph Clancy says he had a "good stern talk" with his staff about why he wasn't told about it sooner.
The story, first reported by The Washington Post, is the latest scandal at the presidential protective service. A spokesman said the agency is aware of the allegations, which are being investigated.
Four months after he was brought back to an agency that was struggling to cope with a series of embarrassing missteps, Joseph Clancy was named permanent director of the Secret Service on Wednesday.
The National Geospatial-Intelligence Agency said one of its employees was operating the quad copter that crashed Monday on the grounds of the executive mansion. The worker was off duty at the time.
The agency says the person who had been operating the device reported that it crashed after they lost control. The White House says the device posed no threat.