A problem with moving parts called interlockings that allow trains to switch tracks appears to have caused a small fire on the tracks around 10:45 a.m., BART spokesman Jim Allison said.
The fire is out and the interlocking problem has been repaired, but BART crews are still working on residual damage caused to the tracks, Allison said.
Trains on the Richmond to Fremont line are running on time, but all other BART lines are experiencing major delays, Allison said.
Some trains are stopping at the 24th Street Mission station in San Francisco and others in Daly City, while shuttle trains are serving all stations south of Daly City, he said.
Allison said around 2 p.m. that there was no estimated time yet for when full service would be restored.