ATTLEBORO - An Attleboro route for a proposed South Coast commuter rail line will have to be re-examined for an environmental permit, but state officials said Monday they still favor another route.

The officials said the preferred route for the new commuter rail line - which, if built, would bring MBTA trains to New Bedford and Fall River - is still through Raynham, Easton and Stoughton.

Town fathers in those communities are fighting the rail line, saying it will disrupt their neighborhoods and damage the environmentally sensitive Hockomock Swamp.

They are asking that alternative routes through Attleboro or Middleboro be used, instead.

But, Eric Abell, spokesman for the state Executive Office of Transportation, said Stoughton is the way to go. "We're confident that the Stoughton alternative is the best route and will result in the highest ridership," he said.

There are problems with all three possible routes.

Going through Attleboro would involve having the trains cross several roads in Taunton, Norton and Attleboro, tying up traffic and creating public safety hazards, critics charge.

State Rep. John Lepper, R-Attleboro, said the grade crossings would make for an unmanageable situation.

"You've got to be nuts to go that way," he said.

State Sen. James Timilty, D-Walpole, said the Attleboro route is too long and would not attract enough riders to make the rail line feasible.

He and Lepper also said the route would join with the crowded Attleboro-to-Boston line that is already heavily used by the MBTA and Amtrak and cannot handle more trains.

Lepper expressed doubts about the state's ability to pay for the $1.4 billion South Coast line to New Bedford and Fall River, regardless of its costs.

He said Gov. Deval Patrick has not adequately explained how the state is going to pay for the construction and operation of the new line.

Timilty went even further, saying bluntly that he is opposed to all three alternate routes because of the cost. Timilty said he had just come from a hearing on transportation issues during which he said he learned that the MBTA is suffering a "crushing debt."

The Legislature voted a few years ago to dedicate one cent of the state's 5 percent sales tax to the MBTA, but the move has proven inadequate, he said.

The state can barely afford the transportation system it has without taking on another $1 billion in costs for the South Coast line, he said.

"We just can't afford it," he said. "We have too many other priorities."

Fall River and New Bedford officials have been demanding commuter rail services for 20 years, saying it holds the key to economic development in their struggling cities, two of the state's larger municipalities.

Four previous governors promised those cities rail service to the two cities, but never delivered. Patrick has pledged he would keep his promise.

Abell said an environmental impact permit for the rail project is scheduled to expire soon, so all three routes will have to be examined once again.

However, he said the state is confident the Stoughton route will emerge as the best alternative again, and a solution to the Hockomock Swamp issue will be found.