Transportation officials warned today that the proposed Commuter Rail link between Boston and the South Coast could be more than $1 billion over budget, according to new estimates.

Permitting issues and new construction cost estimates suggest long promised service to New Bedford and Fall River could take five additional years to get up and running.

The project was most recently set to begin service in 2022 with a $2.23 billion price tag. That figure has risen to $3.4 billion with service set back to 2028 or 2029, according to a report presented to the MBTA Fiscal Management and Control Board Monday.

The T's board was told that if the line were to travel the preferred route through Stoughton, it could be a billion over budget. An alternative plan to shift service onto the existing Old Colony line through the South Shore via the Middleboro station is seen as more affordable, but it won't offer as much rider capacity as the preferred Stoughton route.

The project to build through Stoughton has become bogged down by the the Hockomock Swamp, a large wetland that would require expensive bridge construction.

The MBTA board will consider proceeding or reworking the plan in the coming months. No firm decisions were made at Monday's meeting, but board members requested more information to base their eventual decision on.

Transportation Secretary Stephanie Pollack told reporters MBTA staff is going to prepare a more thorough report for the board to review in 30 days. In the meantime, the T is holding off on public feedback sessions in the New Bedford and Fall River areas until the board can settle on a specific plan.

"We're not pausing or putting the project on hold, we're just making sure we don't have the public conversation until we can hear out all the public feedback the board's going to want to hear from folks on the South Coast," Pollack said.

Pollack said it's worth the additional time to determine the most cost-effective way to get service to the South Coast.

"The [Baker] Administration is committed to the project. I'm committed to the project. What's not clear is the path forward that delivers rail service to the South Coast the soonest."

Sen. Marc Pacheco, a Taunton Democrat, told reporters during the meeting that South Coast Rail has been the most frustrating thing he's dealt with throughout his public career. Every governor he's served with, Democrat or Republican, has supported the Stoughton-based route, but inevitably progress is derailed.

"If I want to be very, very pessimistic about it and very cynical about the project, which I've become over the years, it's 'okay, what excuse can we use now? to not go forward with the Stoughton route?'", Pacheco said.

Pacheco has asked Transportation officials to provide him with information on how many studies the line has been the subject to over the past few decades, and how much taxpayer money has gone into them.

The MBTA's extension of the Green Line into Medford faced a similar cost overrun earlier this year. That project, which relies heavily on non-refundable federal dollars, was saved from cancellation by slashing the scope of the project and contributions from Cambridge and Somerville. Don't expect similar bailouts from the blue collar South Coast cities of Taunton, Fall River and New Bedford.