National passenger rail operator Amtrak said it and the Massachusetts Bay Transportation Authority commuter rail system reached a new agreement covering operation, maintenance and shared use of the MBTA’s 37.9-mile Attleboro Line between Boston and the Rhode Island state line, formally ending a long-running dispute over sharing its costs.

The line is part of the heavily traveled Northeast Corridor, a series of rail segments used by Amtrak, regional carriers and freight lines. Amtrak said about 2,200 of its trains, plus commuter and freight trains operate on some portion of the Washington-Boston route each day.

The MBTA – also known as the “T” – is a unit of the Massachusetts Department of Transportation, with its operations overseen by the 11-person MassDOT board of directors. Transportation Secretary Stephanie Pollack is a board member.

The MBTA owns the Attleboro Line’s right of way and two of three stations that agency shares with Amtrak. It said that a 2003 agreement had allowed Amtrak to use the line with limited priority for its trains, for which Amtrak in return maintained infrastructure and handled dispatching operations.

However, Congress in the 2008 Passenger Rail Investment and Improvement Act, or PRIIA, created the Northeast Corridor Commission and required development of a commuter and intercity rail cost allocation policy, after which Amtrak demanded annual cost-share payments from the MBTA starting with $19 million for fiscal 2016.

The MBTA rejected that demand and filed suit. But the two sides negotiated and concluded a detailed agreement last December; however, it took until now for them and oversight bodies to finalize the accord.

Under it, Amtrak said it will provide maintenance-of-way and dispatching services on the line through 2021, while the MBTA assumes responsibility for directing the Attleboro Line’s capital program that both will invest in.

Amtrak added that the “MBTA and Amtrak will contribute to capital projects and operating costs” in a manner consistent with PRIIA and the cost allocation policy. And “Amtrak will allow the MBTA to use South Station’s system for dispatching of the south-end branch lines, charging for its use of these facilities based on a proportionate sharing of facility and system costs.”

According to a June MBTA presentation to its oversight Fiscal and Management Control Board, the MBTA will pay Amtrak about $9.8 million this year for operations and capital costs, with the payment rising to $22.2 million next year. Amtrak will pay at least $5.8 million next year in capital costs, while the MBTA expects to recover at least $1 million from Rhode Island for service into that state.

That presentation said the new accord, which runs through Sept. 30, 2021, also reduces the MBTA’s indemnification obligation for incidents and “tightens Amtrak’s indemnification requirements in Massachusetts.”

And it clarifies that Amtrak’s approval is not needed for the MBTA’s capital projects in the Attleboro Line right of way.