BART said it was restarting service between two stations early Sunday afternoon after stopping trains from passing through the area.
BART spokesperson Cheryl Stalter said in a statement at 9:45 a.m. that service between the Balboa Park and Daly City stations was being halted due to police activity.
The decision came after that activity first caused delays of about 10 minutes before increasing, Stalter said.
A San Francisco Fire Department spokesperson said firefighters were "working with multiple public safety agencies to investigate a report of a subject on the tracks" between the stations and asked residents to avoid the area.
By 1:30 p.m., service was back to normal on the system's Blue Line between Daly City and Dublin-Pleasanton stations and Green Line between Daly City and Berryessa-North San Jose, with a 20-minute delay still remaining on the San Francisco line.
Mutual aid service by Muni allowed passengers to use the Nos. 14 and 14R lines to travel between Balboa Park and Daly City stations.
The San Francisco Police Department did not immediately respond to The Standard's request for comment.
BART initially said Sunday morning that three of the four lines that go through San Francisco were out of service. Only the Yellow Line, which runs between Antioch and SFO, was operating.
At that time, passengers on the system's Red Line were asked to board an Antioch-bound train and transfer to Richmond-bound trains at Oakland's 19th Street Station. Passengers on the system's Blue Line were asked to board Antioch-bound trains and transfer to Berryessa trains at Oakland's 12th Street/City Center, and at Bay Fair Station to a Dublin-Pleasanton train. Green Line riders toward Berryessa were asked to board an Antioch-bound train and transfer to a Berryessa train at the 12th Street Station.