San Francisco police say magnetometers set up by the Secret Service detected the firearm Tuesday morning.
According to authorities, the employee had recently moved from Texas where carrying a concealed firearm is permitted.
A background investigation found he had an arrest warrant pending out Tarrant County - outside Dallas.
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Harris left the Fairmont Tuesday afternoon without incident.
The Secret Service says the vice president was not a target or under any threat.
Vice President Harris' visit to the Bay Area was her first time back since her election loss.
Harris and the Second Gentleman flew here following a vacation to Hawaii.
The reason for their visit was unclear.