The incident was reported at 10:21 a.m. between the Castro and Forest Hill stations, and involved an outbound one-car KT-Ingleside/Third Street train, said John Haley, the agency's director of transit.
The train had been stopped at the Castro station to let passengers on and off, and while it was in the station there was a problem with one of the doors, Haley said.
The operator got off the train to check on the door, which then closed, and the train began moving in automatic mode with the operator still on the platform, Haley said.
About 30 passengers were on the train as it traveled about a quarter-mile toward the Forest Hill station before someone pulled an emergency lever on board, causing the vehicle to come to a stop, according to Haley.
He said that pulling the emergency lever was "an understandable reaction" from passengers, who did not know that the train could operate on automatic controls without an operator on board.
Haley said investigators will look into whether the operator pressed a red mushroom-shaped emergency brake button on the train before getting off to check on the door.
He said pressing that button before leaving the train is standard Muni procedure, and that if it had been pressed, "the train couldn't have moved."
The driver has been placed on non-driving status pending further investigation into the incident, Haley said.
The train was moved to the Forest Hill station then taken out of service so crews could check whether there were any problems with it, he said.
No one was injured in the incident, and Haley credited the passengers for staying on the train while it was stopped in the tunnel between the stations.
"It was a major help in terms of protecting their own safety," he said. "It would be much more problematic if people had gotten out."
Passenger describes being trapped on unmanned Muni train
Passenger Susan Moore told ABC7 News when they realized there was no driver, and smelled something burning, someone pulled the emergency brake. The train then came to a stop about a quarter mile from the station inside the tunnel.
"They were pushing buttons to talk to the driver, there was no driver, both muni driver doors were locked and they were trying to get them open," said Moore.
There was no cellphone service and no communication from the outside.
"We didn't know if a train was going to come up, so a couple guys went in the back and it was kind of like we were on our own without any help from Muni," said Moore.
Muni says when the train stopped, the control center was alerted, a mechanic was there in 12 minutes and drove the train to the Forest Hill Station. Muni says passengers were never in danger.
"Once the train was stopped, not only did the controllers respond immediately, but we also stop all trains in both directions around it to increase the safety zone," said Haley.
"For Muni to make light of it, it was really upsetting because it was like you know what? You weren't there," said Moore.
Moore says she will keep riding Muni, but might do a double-take if the driver gets out.
ABC7 News reporter Heather Ishimaru contributed to this report.