San Francisco Police Department (SFPD) initially posted messages on Twitter social network that its bomb squad was on the scene assisting the probe after receiving notification of a vehicle, and public is advised to shelter in place.
However, at about 2:30 p.m. local time, SFPD said the scene near the city's Hall of Justice was safe and streets would reopen in the area.
ABC7 News showed video footage of a robot apparently trying to open the vehicle's trunk, and a source told the ABC network local affiliate that the car had a note on a window claiming there was a bomb.
The car was in a tow yard underneath Highway 80, which has heavy traffic most time of the day heading into San Francisco or out toward the East Bay city of Oakland across the historic Bay Bridge.
Among locations closed as a precaution was the Hall of Justice, which serves as SFPD's operational headquarters, the main San Francisco County Jail, as well as base of operations and headquarters for the San Francisco Sheriff's Department, and garage for the majority of SFPD vehicles. The building was evacuated and court cancelled.
SFPD spokeswoman Officer Giselle Talkoff talked with media but did not provide details.