New Bedford officials are threatening to sue the MBTA on a claim the transit agency wrongly seized city land to construct the South Coast Rail project, casting new uncertainty onto a $1 billion project that’s labored through decades of fits and starts.

In a draft complaint the city sent to the MBTA in April, attorneys for New Bedford argued that land seized for the rail project should be “invalid’’ because New Bedford was not yet part of the MBTA’s service district, according to a copy obtained by the Globe. If filed, the suit would seek to have the land returned to the city.

It was not immediately clear when, or if, the city would file the suit. New Bedford also believes the MBTA should be paying more for the properties, claiming in the draft complaint that its offer is “grossly inadequate’’ given the millions the city spent remediating the land. MBTA officials told the Globe they paid New Bedford $486,627.

New Bedford Mayor Jon Mitchell declined to comment through a spokeswoman. A spokesman for the Massachusetts Bay Transportation Authority on Friday defended taking the land, where the T is putting one of two new stations, parking spaces, and a train layover site.

“The MBTA appropriately exercised its eminent domain powers as provided by the Legislature and paid fair market value for all the properties taken,’’ spokesman Joe Pesaturo said.

The city’s lawsuit would be an unusual challenge of the T’s eminent domain authority, an area where litigation typically focuses on a property’s worth, attorneys and former state officials say. Even the consideration of a lawsuit surprised state lawmakers after New Bedford officials spent years advocating for the project alongside local business leaders and others.

Challenging the legality of the T’s seizures themselves would be an “interesting little twist,’’ said Peter Flynn, a veteran eminent domain attorney who last year represented a different New Bedford property owner whom a jury awarded $3.51 million, roughly $1.2 million more than what the MBTA originally paid that owner for other land it seized for the South Coast Rail project.

“If there is a challenge to the validity, it does put a pall of uncertainty over that project,’’ said Flynn, a former assistant attorney general. “If the MBTA proceeds on course and [a judge determines] they didn’t have the right to do what they’re doing, they’re doing that project at their peril.’’

Jim Aloisi, a former state transportation secretary, called the draft complaint “pretty extraordinary.’’

“This seems to be about money,’’ he said of the dispute. “But if you advocate and lobby for [the rail connection], the idea that you’d now be taking this action against the very entity you’ve been asking to do this . . . it’s biting the hand that fed you, in a way.’’

The South Coast Rail project, which would restore commuter rail service to the region for the first since the 1950s, has a tortured history, marked by stalled planning and warnings about ballooning costs. But it gained traction in recent years after then-governor Charlie Baker’s administration embraced a plan to split the construction into phrases.

In 2019, the state — not the MBTA — said it would pick up the roughly $1 billion tab for the first phase of extending commuter rail service from Boston through Middleborough to New Bedford and Fall River.

The MBTA said last year that service is expected to start in late 2023, though officials have yet to set a formal date. It’s expected to take riders from Fall River and New Bedford about 90 minutes to reach Boston.

The T is constructing two stops in New Bedford for the project, one on Church Street and one near downtown, as well as a layover facility to store trains overnight.

But the city and the T are at odds over the value of the land the T seized. Portions of it were once part of the city’s “railroad depot project’’ site, which the city said it spent $17.3 million cleaning up, according to the complaint. After cobbling together insurance and other reimbursements, the net cost to the city was $9.9 million, the city said.

The MBTA’s offer amounted to a “fraction’’ of the city’s costs, according to the complaint.

The MBTA has used eminent domain for decades to take land. The T and other public bodies can seize land as long as they show that it is in the public interest. They then must compensate the property owner for the land’s fair market value.

But New Bedford indicated it’s prepared to challenge more than the price.

The city’s draft complaint, dated April 4 and crafted by lawyers from the Hingham firm Drohan Tocchio & Morgan, targets a series of land takings the T executed in 2020 and 2021. But in order for the T to build or expand any “mass transportation facilities,’’ the land itself had to already be “in the territory of the authority,’’ according to the complaint. At the time, the city was outside the MBTA’s service district; New Bedford residents voted to formally join the MBTA in November 2022.

As a result, the city argued, the T “lacked authority to both provide for such construction, and to make the identified takings,’’ and the court should return the land to the city.

Even the potential for litigation set off alarm bells among the rail project’s supporters. “First off, I’m shocked,’’ said state Representative Chris Markey, a Democrat from nearby Dartmouth. “The act of actually drafting up a complaint means they’ve invested some time into it. I’m kind of perplexed.’’

State Representative William Straus, a Mattapoisett Democrat who co-chairs the Legislature’s Transportation Committee, said the legal theory New Bedford is threatening “is a dangerous one’’ that could have a chilling effect on other MBTA expansion projects.

“If you’re threatening a lawsuit, it’s hard to see how that benefits New Bedford’s long-sought goal — and I’m talking 30, 40 years — to reconnect to the commuter rail,’’ he said. “I hope [the T] does not entertain this as a serious demand.’’

Mitchell has vocally supported the project in the past, noting the city will not have to pay extra for the commuter rail to extend there. But he and others have also questioned how often residents will utilize it after the state opted for a slower route instead of building through the Hockomock Swamp, as initially considered.

In 2017, state officials projected the South Coast line could initially see 3,220 one-way trips — or about 1,600 riders taking a round trip. Yet, it’s unclear whether those pre-COVID-19 figures will hold as more people embrace remote work.

“I’m a big supporter of the project, but I also think the public needs to be realistic about its benefits,’’ Mitchell told The Public’s Radio last year. “An indirect route to Boston on the rail is not going to usher in prosperity.’’

Brian Kane, executive director of the MBTA Advisory Board, said while he believes the T’s eminent domain powers extend statewide, “that’s never been tested.’’ He said he also was confident the project wouldn’t be derailed.

“The people of New Bedford, if you will, have spoken. It will happen,’’ he said. “It’s going to be a question of money, I guess.’’

Matt Stout can be reached at matt.stout@globe.com. Follow him on Twitter @mattpstout.