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(The following story by Anthony Flint appeared on the Boston Globe website on January 4.)

BOSTON — The US Army Corps of Engineers has issued a sweeping environmental permit allowing work to proceed on the Greenbush commuter rail restoration through the South Shore, the last significant hurdle for the controversial $479 million project, state transportation officials said yesterday.

The 120-page permit, which MBTA officials picked up yesterday at the New England office of the federal agency in Concord, clears the way for construction of the Greenbush line in environmentally sensitive areas along the 18-mile rail corridor.

State Transportation Secretary Daniel A. Grabauskas said work would begin immediately along sections of the route in Braintree, Weymouth, and Hingham. An administrative magistrate has dismissed appeals filed by project opponents of state-issued wetlands permits in those communities. Only a challenge to state permits in Cohasset and Scituate remains.

“We can get to work on a significant portion of the right-of-way now,” Grabauskas said. “The MBTA is doing this project in the most environmentally sensitive manner possible, being mindful of endangered species, wetlands, and historic districts. All these appeals have cost us time and money.”

John Bewick, spokesman for the Hingham-based residents group Advocates for Transportation Alternatives, which opposes the Greenbush project, said that “it is not clear until we have a chance to read it what our actions will be.” He did not rule out an appeal of the Army Corps permit.

Any such appeal would have to be filed in federal court. The Army Corps of Engineers has jurisdiction over any construction work proposed for federally designated wetlands. The state separately issues permits for work through areas it defines as wetlands.

“This is not a surprise,” Bewick said of the granting of the permit. “Nothing has changed the fact that Greenbush is fiscally irresponsible, at a cost of $350,000 per car removed from rush hour, at a time when the T is curtailing bus service and cutting ferry service in the harbor and is obviously in a fiscal crisis.”

The T recently said it might have to cut its Night Owl, a late-night bus service, as well as regional, privately operated bus lines to help close a $16 million budget gap for the current fiscal year. The Greenbush restoration would be funded from the T’s capital budget and is not eligible for federal money.

Bewick said a thorough review would show the project is “environmentally damaging, compared to alternatives.”

“They are required to do a full environmental review, and obviously they haven’t,” he said.

No one at the Army Corps of Engineers New England office could be reached for comment yesterday.

Joe Pesaturo, spokesman for the Massachusetts Bay Transportation Authority, said that opponents of the project “should see the writing on the wall.”

The Greenbush commuter rail line stopped service in 1959, as the Southeast Expressway opened. The T has sought to put trains back on the line, to complete the three branches of the Old Colony line, which reaches into the South Shore and Southeastern Massachusetts.

The project was put on hold in 2003 because of concerns about rising costs, including a $90 million tunnel that must be built under Hingham Square. Although some advocates said that urban transit would be a better investment, Governor Mitt Romney went ahead with the project, in part because it is one of the transit improvements the state promised to undertake as a condition for receiving federal funding for the Big Dig project.

The T says the line would carry 8,400 riders per day, relieve congestion on Route 3 and the Southeast Expressway, and reduce car pollution. Opponents say that putting big commuter trains on reconstructed tracks along the corridor will be destructive for houses and wetlands areas adjacent to a railbed that has been inactive for more than four decades.