As of noon, 10- to 15-minute delays were reported systemwide.
The fire occurred shortly before 8 a.m. between the Civic Center and Powell Street stations, BART spokesman Linton Johnson said.
The small blaze was quickly extinguished but not before it knocked out the sensors that track the trains through that portion of tunnel, Johnson said.
As a result, the system is registering a "ghost train," in that spot. The "ghost train," meant to simulate an actual train, ensures that trains in automatic mode don't get too close to each other in cases where there may be blockage on the tracks, Johnson said.
There is no actual blockage, but trains are being forced to run in manual mode at 25 mph or less between the Powell Street and 16th Street stations.
"It's just like being on a freeway where normally you're doing 55 and suddenly, for whatever reason, everyone's slowing down to 20 and you've got a big backup," Johson said.
To avoid a severe traffic jam in the system, trains are being turned around at a number of spots systemwide.
There is no service from Richmond to Millbrae, Johnson said. Passengers headed to Millbrae need to transfer to an SFO-bound train then take a shuttle from SFO to Millbrae.
Trains coming from Dublin-Pleasanton are stopping and turning around at San Francisco's Montgomery station.
Fremont-to-Daly City trains are only going as far as the MacArthur station. Passengers heading toward Daly City on that line should transfer at the Bay Fair or MacArthur stations.
Trains on the Pittsburg/Bay Point line are traveling their normal route, as are trains on the Richmond-Fremont line.