After problems with an Amtrak-owned signal system near South Station delayed or canceled 40 MBTA commuter trains Sunday, the state Transportation Department and the MBTA will pursue fining Amtrak for service disruptions in the future, Transportation Secretary Stephanie Pollack said Monday.
The Massachusetts Bay Transportation Authority is renegotiating its agreement with Amtrak, the federally subsidized passenger rail service, over the use and maintenance of the MBTA’s tracks between Boston and Rhode Island, a portion of the heavily traveled Northeast Corridor.
Pollack said state officials feel obligated to pursue fines in the new contract after Amtrak’s maintenance work on a South Station signal system delayed passengers on Sunday.
Two months ago, the same damaged signal system prompted the rerouting of thousands of commuters away from South Station for an entire day.
“If they continue to act in ways that make it impossible for us to run our commuter rail system, why shouldn’t they owe us some form of penalty?” Pollack said.
Chelsea Kopta, a spokeswoman for Amtrak, apologized to riders for the delays, but declined to comment on the possible fines.
“We do not negotiate contracts in public but welcome any and all proposals designed to enhance the service for all rail passengers in the [Northeast Corridor],” Kopta said.
The strong words from the state’s top transportation official come as the two transit agencies continue to butt heads in and out of court over who should pay for the maintenance and use of Amtrak-owned signal systems in use on the T’s tracks.
Under an agreement signed in 2003, Amtrak has used, maintained, and dispatched trains on the Attleboro line — the MBTA tracks between Boston and the Rhode Island line — for free. But after a change in federal policy in late 2015 required states to help pay for Amtrak’s work on the track along the Northeast Corridor, Amtrak asked the MBTA for approximately $30 million a year.
In response, the MBTA in January sued Amtrak and the commission that helped develop the new rule, arguing that Amtrak would be in breach of an agreement already in place, and that the new policy was unconstitutional.
Amtrak then terminated the agreement, and continues to negotiate with the T over a new deal as the lawsuit is ongoing.
Pollack has said the MBTA should not be liable for paying for such fees because it allows Amtrak to use its tracks.
Kopta said Amtrak does not comment on pending litigation but noted that new rules require states to pay for some of the maintenance costs.
Tensions over the negotiations and the lawsuit have appeared to spill into the public arena in recent months.
The MBTA has been pointed about explaining which agency is responsible for delays out of South Station, repeatedly releasing public statements noting that the broken signal system software is “Amtrak-owned.” On Sunday, the T publicly rebuked Amtrak for failing to notify officials about maintenance work that helped lead to the delays.
Amtrak maintains the computer system near South Station that sends electronic commands to the 63 switches that allow trains to switch tracks.
In February, Amtrak maintenance work on a Wednesday night led to the system’s failure the next morning. Instead of going through South Station, MBTA trains were rerouted away from the transit hub, disrupting the commutes of thousands.
On Monday, Pollack explained that a similar problem with the same system happened during the weekend: After Amtrak performed maintenance on the system on Saturday night, workers were unable to reboot the system Sunday morning.
In all, 32 commuter rail trains were delayed and eight runs were canceled, out of 60 scheduled trains on Sunday, according to Jacquelyn Goddard, a Transportation Department spokeswoman.
Pollack said the widespread delays were particularly troubling because thousands of runners and visitors had flocked to the area for Monday’s Boston Marathon.
Pollack said state officials now want Amtrak to notify the MBTA about its maintenance schedule, so the agency can be more prepared for any failures from Amtrak. She said the MBTA had not been notified about the possibility of the widespread failures on Sunday morning before they happened.
“What is clear from this incident, as well the prior one, is that we need provisions in the contract that ensure the MBTA and its riders will get advance notice,” she said.
Pollack said it was “unfortunate” that the MBTA had to turn to fines.
“But, for whatever reason, this has now happened twice in this calendar year,” she said. “The MBTA is working hard to improve their performance and providing reliable on-time service to riders, and we can’t have the Amtrak interfering.”
Since 2015, the T and the operator of its commuter rail, Keolis Commuter Services, have been under pressure to improve performance after service was disrupted for weeks amid record-breaking snowstorms. A spokeswoman for Keolis said it would defer all comment to the state.
The MBTA’s contract with Keolis also includes a provision for poor service. The T fined Keolis about $7.53 million in its first year for subpar service, but the T eventually allowed the company to use its penalty money to hire more employees and make other improvements.
Some close watchers of the T say similar fines may help commuter rail riders who want better service. Paul Regan, the executive director of the MBTA Advisory Board, said he believes penalizing Amtrak for actions that disrupt service is “absolutely justifiable.”
“There’s a perception that we don’t have much leverage with Amtrak, and any leverage we can get with them is absolutely necessary,” said Regan, whose organization represents the cities and towns that receive MBTA service. “They should absolutely be held responsible for the delays they cause.”
Laura Crimaldi of the Globe staff contributed to this report. Nicole Dungca can be reached at email@example.com. Follow her on Twitter @ndungca.