The incident, which saw the train go 5 miles, began at 6:08 a.m. at the Braintree station on the MBTA's Red Line, south of Boston, when the operator apparently stepped off the train to inspect a signal that was experiencing a problem, said Gov. Charlie Baker.
"There was a signal issue that made it necessary for the operator to request and receive from the operations control center permission to put the train into bypass mode," Massachusetts Secretary of Transportation Stephanie Pollack told reporters. "The operator left the train to execute that procedure. Bypass mode allows the train to depart the station, even if it's not receiving the signal that it would otherwise use to operate on its own."
The requirements to put the train into bypass mode include initiating the full service brake, as well as a hand brake, MBTA Chief Operating Officer Jeff Gonneville said. Whether proper procedures were followed is under investigation.
"Operator error is the current focus of the investigation," Pollack said.
Baker said he is "confident this is an isolated incident, where a single individual has appeared to make multiple errors."
The governor said while he understood "the fear, the shock and surprise that ... passengers must have experienced," commuters should not be afraid to ride the rails.
The operator has been put on administrative leave, pending the outcome of the investigation, Pollack said.
While outside the train, the operator suffered minor injuries after he was struck as the train pulled away, according to MBTA spokesman Joe Pesaturo. No passengers were hurt.
Officials did not indicate how fast the train was going during the ride. Such a ride can typically include from three to six cars.
Transit authority personnel cleared the line ahead of the train and shut off power to the third rail several minutes after it departed the Braintree station, Pollack said.
The train went through four stations before it came to a halt past the North Quincy stop.
A passenger on the train told CNN Boston affiliate WHDH
that the lights went out and the train eventually stopped. Some passengers in the first car knocked on the door of the operator's cabin and got no response, she said.
Passengers pressed emergency buttons and tried to open the train's doors.
"My only concern was people trying to open the train when we don't know what's going on," said rider Fernanda Daly. "There were people even trying to break the windows so we could get out."
MBTA personnel boarded the disabled train and drove it to the next station, where passengers were asked to gather their belongings and leave the train, according to Michael Verseckes, a spokesman for the Massachusetts Department of Transportation.
The train was taken out of service and will remain impounded until the investigation concludes.
Pollack said the incident was an "unacceptable breach of our responsibility to keep our riders safe. ... We failed our passengers today."
Transit police detectives are investigating, officials said.
Baker earlier said an inspection showed some of the controls were manipulated, enabling the train to be set in forward motion. But officials later said that did not appear to have happened.