The Northern New England Passenger Rail Authority is moving ahead with plans to build a layover and maintenance facility for the Amtrak Downeaster at a controversial site in Brunswick, despite the recent loss of a federal grant that would have paid for the project.

Construction of the large industrial shed, initially expected to start this spring, has been delayed for an undetermined period, in part so residents can help develop a plan to diminish the facility’s effect on residential neighborhoods off U.S. Route 1 in West Brunswick.

The lack of a layover facility won’t delay the authority’s plan to provide passenger service to Freeport and Brunswick starting in late 2012, said Patricia Quinn, the authority’s executive director. Trains will continue to be serviced and parked overnight in Portland, where there is no maintenance building.

Without a layover facility in Brunswick, the Downeaster will make two round trips daily from Brunswick to Boston; trains will travel from Portland to Brunswick each morning for a 7 a.m. departure and return to Portland each night after the last stop in Brunswick around 9 p.m.

“We’re going to expand service to Brunswick, and we’re going to continue looking for funding to enhance Downeaster service overall,” Quinn said Tuesday. “Given limited resources, we’re trying to take advantage of all resources available.”

The authority is developing specifications now for the layover facility and plans to seek proposals as early as February from firms that would like to design and build it.

The authority learned earlier this month that the U.S. Department of Transportation rejected its application for $20 million in federal Transportation Investment Generating Economic Recovery, or TIGER, funding.

The department had received applications for 848 projects worth more than $14 billion, but had only $511 million available, enough to fund 46 projects, according to a news release.

The rail authority’s grant application sought funding for three projects that would cost a total of $25 million:

* $9 million to build the layover facility in Brunswick.

* $9 million to build a Y-shaped intersection in Portland, so the Downeaster could serve Brunswick without backing up.

* $7 million to add a second section of tracks at Royal Junction in Yarmouth so trains could pass each other without stopping.

The rail authority planned to cover nearly $5 million of the $25 million needed for the three projects with a combination of state bond and capital reserve funds, Quinn said. Now that money will be used to build the layover facility, she said.

The potential cost and size of the layover facility are unclear now, Quinn said. In July, she said the shed would cost $5 million and measure 40,000 square feet — large enough to hold three passenger trains, each with an engine, several cars and a control car.

The Portland and Yarmouth projects would shave several minutes off the 50-minute train ride between Portland and Brunswick, Quinn said, making the Downeaster more competitive with a 35-minute drive time. She said that’s still the long-term goal, and the projects will be done as funding becomes available. She plans to apply for additional TIGER funding in 2012.

The authority has received several federal grants in recent years, including $38 million to improve tracks and crossings north of Portland and build platforms in Freeport and Brunswick; $21 million to add a 10-mile section of double track between Wilmington and Andover, Mass.; and $500,000 to create a service development plan for the Downeaster.

The authority plans to build the layover facility in Brunswick on the north side of the tracks, between Church Road and Stanwood Street.

The authority’s board of directors decided to buy the site in August, Quinn said, after consultants reviewed other sites on Farley Road and in the Brunswick Industrial Park. The Maine Department of Transportation bought the site in September from Pan Am Railways for $268,950, she said.

An advisory group, including several community members, has started working on a plan to mitigate noise and other environmental effects that the facility may have on neighbors.

State Sen. Stan Gerzofsky, D-Brunswick, said Quinn and other authority officials may want to reconsider other sites when they see the costs associated with reducing the facility’s effect on residential neighborhoods near the “preferred location.”

“The community is going to be much more involved in just how that facility is going to work,” Gerzofsky said. “We want train service to Freeport and Brunswick, but we really want to do things right.”

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