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This story was updated at 7 p.m. on June 27.

RUNNING RAIL SERVICE from South Station to New Bedford and Fall River will take five years longer and cost $1 billion more than previously projected, state transportation officials said on Monday.

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The South Coast Rail numbers were eerily similar to the MBTA’s announcement that the Green Line Extension from Lechmere into Somerville was going to cost $1 billion more than earlier projections. The T responded to the spiraling cost of the Green Line Extension by redesigning the project and seeking additional funding from communities that would benefit. The final go-ahead on that project is contingent on the federal government’s willingness to stand by its $1 billion investment in the project.

With South Coast Rail, Transportation Secretary Stephanie Pollack said the state could continue with its original plan to run service to New Bedford and Fall River from the terminus of the Stoughton commuter rail line. She said that project is currently projected to cost $3.4 billion, up from an earlier estimate of $2.23 billion, and not launch service until 2029. Or, Pollack said, the state could pursue an alternative route that has the potential to offer service in six to eight years at far less cost. The tradeoff is that fewer trains would run on a daily basis with the alternative route and the run itself would take 91 instead of 77 minutes.

Pollack stressed that the alternative route using the existing Middleboro/Lakeville commuter rail line has not been fully vetted yet, so cost projections could change. “It is really a concept,” she said. “It is not a project.”

Pollack on Monday asked the MBTA’s Fiscal Management and Control Board for advice on how to proceed, but it seemed as if the board members were wary of weighing in quickly on such a politically sensitive topic. Board Chairman Joseph Aiello seemed underwhelmed by the projected ridership numbers of 4,750 people per day, suggesting they averaged out to about 100 people per train. Others on the board said they wanted to cost out the Middleboro option and also explore running dedicated bus service from the South Coast to Boston or to the terminus of a commuter rail line. The vetting process could take much of the summer.

Sen. Marc Pacheco of Taunton, a supporter of South Coast Rail, said all the possible routes have been reviewed three different times by three different gubernatorial administrations and each time the conclusion was that the Stoughton route was the best. He said he suspected the latest indecision by the Baker administration reflects a reluctance by the governor to follow through on a campaign promise. “They’re looking for a way out,” he said outside the room where the Fiscal Management and Control Board was meeting.

Steps away, Rep. William Strauss of Mattapoisett, the cochair of the Legislature’s Transportation Committee, said it was only prudent that state officials review all possible options before getting too far down the road with South Coast Rail. He said he worried that even the administration’s latest projections could be conservative because of all the hurdles the project would face in obtaining local approvals for environmental variances.

Strauss, who commutes to Boston regularly from the South Coast area, said even at more than 90 minutes the commute via Middleboro would be attractive to someone like him.

South Coast Rail has been talked about since 1994 as a way to bring New Bedford and Fall River into the orbit of Greater Boston’s economy. The project has always been a high priority of lawmakers from the South Coast region and a political priority of most governors, even though there have been persistent concerns about the high cost of the rail line and projections about relatively few riders.

Gov. Charlie Baker, during his last run for office, promised to build South Coast Rail. He has stood by that pledge, even as his priorities have shifted. He has said he wants to focus on maintaining and improving the existing transit system rather than expanding it.

State officials have always portrayed South Coast Rail as a long-term project, one where work would be done as money became available. But as the T prepared to expend larger amounts of money on South Coast Rail, a review was undertaken, and it was discovered that a lot of environmental permits for the project would probably take longer to obtain than previously forecasted.

South Coast Rail as currently envisioned would run along the existing Stoughton commuter rail line and from there go on to Taunton and then on to Fall River and New Bedford. That route required the purchase of rail rights between Stoughton and Taunton, the purchase of new electric locomotives and rail cars, and lots of environmental mitigation because the tracks would run through a sensitive swamp area.

Pollack and Frank DePaola, the T’s general manager, said the Patrick administration failed to move the permitting process along after the project obtained initial Army Corps of Engineers approval. “We really don’t have any permits yet on this project,” DePaola said.

In the original design, environmental permitting was scheduled to take 3.5 years, but that estimate has been increased to anywhere from 4.5 to 6.5 years. DePaola said the project would require nine wetland variances and project-wide mitigation. He said every month of delay increases the cost of the project by $4.1 million. The new projections were developed with the help of a construction team and an independent cost estimator.

Overall, the project is now expected to cost $3.4 billion, up from the original $2.23 billion estimate. So far, DePaola said, $24 million has been committed for South Coast Rail, but only $18 million expended.

Pollack said the numbers are pretty clear for residents of the South Coast looking for rail service. “They’re not going to see it for a long time and much longer than they expected,” she said.

Pollack said one option for policymakers to consider is providing service on the Middleboro-Lakeville commuter rail line, connecting at its terminus to an existing line that goes to Taunton, and from there down to Fall River and New Bedford. Pollack said that route avoids many of the environmental problems associated with the Stoughton approach, but had been rejected earlier because only one track is available on that line between Braintree and South Station where a number of commuter rail lines converge. That bottleneck means there could only be four peak-period trips each during the morning and evening rush hours and 28 trips daily as opposed to 40 trips daily with the Stoughton design.

Meet the Author Bruce Mohl Editor , CommonWealth About Bruce Mohl Bruce Mohl is the editor of CommonWealth magazine. Bruce came to CommonWealth from the Boston Globe, where he spent nearly 30 years in a wide variety of positions covering business and politics. He covered the Massachusetts State House and served as the Globe’s State House bureau chief in the late 1980s. He also reported for the Globe’s Spotlight Team, winning a Loeb award in 1992 for coverage of conflicts of interest in the state’s pension system. He served as the Globe’s political editor in 1994 and went on to cover consumer issues for the newspaper. At CommonWealth, Bruce helped launch the magazine’s website and has written about a wide range of issues with a special focus on politics, tax policy, energy, and gambling. Bruce is a graduate of Ohio Wesleyan University and the Fletcher School of Law and Diplomacy at Tufts University. He lives in Dorchester. About Bruce Mohl Bruce Mohl is the editor of CommonWealth magazine. Bruce came to CommonWealth from the Boston Globe, where he spent nearly 30 years in a wide variety of positions covering business and politics. He covered the Massachusetts State House and served as the Globe’s State House bureau chief in the late 1980s. He also reported for the Globe’s Spotlight Team, winning a Loeb award in 1992 for coverage of conflicts of interest in the state’s pension system. He served as the Globe’s political editor in 1994 and went on to cover consumer issues for the newspaper. At CommonWealth, Bruce helped launch the magazine’s website and has written about a wide range of issues with a special focus on politics, tax policy, energy, and gambling. Bruce is a graduate of Ohio Wesleyan University and the Fletcher School of Law and Diplomacy at Tufts University. He lives in Dorchester.

DePaola said recent discussions with a contractor who was interested in partnering with the state on expanding the Southeast Expressway raised the possibility of eliminating the one-track restriction from Braintree in. The big hurdle for adding a second track on that section is the area around Savin Hill Station, where there is no extra room. The contractor looking to expand the Southeast Expressway, however, suggested burying underground at about 4,000 feet the commuter rail and Braintree-line MBTA tracks, which could allow the addition of an extra commuter rail track.

No one knows how much the Middleboro approach with the addition of a second commuter rail track between Braintree and South Station would cost. DePaola, who is retiring, estimated the cost of the Middleboro approach would be “significantly less” than the Stoughton approach.

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