BOSTON (CBS) — MBTA officials say the investigation into the runaway Red Line train Thursday morning is focused primarily on operator error.

“We failed our passengers today,” said Transportation Secretary Stephanie Pollack.

Pollack said the operator was initially unable to start the train at Braintree Station and received clearance to put the train into bypass mode. The operator then exited the train, which kept rolling with about 50 passengers on board.

Related: Passengers Recall Dangerous Ride

Pollack said a full-service brake and hand brake are required to be engaged before a train goes into bypass mode, and that it was unclear if both had been engaged before the operator left the train.

Pollack said the incident “represents an unacceptable breach of our responsibility to keep our riders safe.”

The 6:08 a.m. inbound train traveled through four stations. The train was brought to a halt just past North Quincy Station, when crews powered down the third rail.

At that point, T employees boarded the train, driving it to the JFK/UMass stop to allow passengers to exit. The train was taken out of service and examined.

Pollack said that it took about nine minutes after the incident was reported to stop the train.

Train operator David Vazquez suffered minor injuries after he exited the train and was struck. He has been placed on administrative leave pending the outcome of the investigation. Vazquez, 51, has been with the MBTA for more than 25 years.

No passengers were injured.

Only one operator is on each train. The Boston Carmen’s Union released a statement saying “Creating extra precautions and having a second employee, such as a train attendant or guard, assigned to these trains could have avoided this incident.”

Pollack says the Red Line previously had two operators on each train, but “if safety procedures are followed properly, there is no safety problem with operating trains with a single operator.”

A person with knowledge of the trains told WBZ-TV’s Lauren Leamanczyk this was a “very dangerous situation for passengers.”

Initial indications were that a safety device inside the train’s cab may have been tampered with.

“At this point we believe this was an isolated incident,” Gov. Charlie Baker said in a press conference in Plymouth.

Gov. Charlie Baker Addresses Red Line Incident

Baker added that an inspection of the train found the controls had been “manipulated.”

“The discussion that’s going to take place on our end is negligence versus something else,” Baker said.

The FBI confirmed that it is aware of the incident and has been in contact with Transit Police. The Federal Transit Administration is sending an investigator to participate in the investigation being led by the Massachusetts Department of Public Utilities.

Passenger Fernanda Daly told WBZ-TV’s Beth Germano that when the lights went out on the train, riders knocked on the booth but found no conductor inside.

“The whole train started going slow, the lights went off and everything just stopped down between Quincy and JFK and we stayed there for about 30 minutes,” the female passenger said.

“It was all dark, everything was quiet. It was just us. We had no idea what was going on,” Daly said.

Some people attempted to break windows, while others attempted to pry open the doors, according to Daly.

Similar Incidents Around The Country

So how often does a public transit train take off with no one at the controls?

WBZ sent an inquiry to the Federal Transit Administration. Late Thursday, a spokesman for the agency provided two recent examples.

WBZ-TV’s Ryan Kath reports

In September 2013, an unmanned train belonging to the Chicago Transit Authority Heavy Rail left the yard and entered a live track. It ended up colliding with a train carrying passengers. The crash injured 33 passengers along with the operator of the train. The incident was blamed on a maintenance issue.

The other example provided sounds very similar to what MassDOT officials described in Boston.

This past February, an unmanned train for the Sacramento Regional Transit District Light Rail left the yard after a mechanic bypassed the deadman safety control while troubleshooting a problem. The mechanic then stepped off the train, which took off. The train derailed, then reconnected with the tracks before eventually coming to a stop. The incident resulted in $70,000 in property damage.

The big difference between those examples and what happened on the MBTA Red Line train on Thursday: neither of those unmanned trains were also carrying passengers.

WBZ NewsRadio 1030’s Bernice Corpuz reports

WBZ-TV’s Ryan Kath contributed to this report.

Comments (21)