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AYER — The proposed joint rail venture involving Billerica-based Pan Am Railways Inc. intends to build a new automotive facility at the former San Vel property off Willow Road, according to a filing with the federal Surface Transportation Board.

Plans for the new railroad parking lot, which would store up to 810 automobiles near the town’s water supply, were filed May 30 as part of Pan Am’s proposal with Virginia-based Norfolk Southern Railways to form a joint venture to be called Pan Am Southern.

The new company also proposes to use capital from Norfolk Southern to complete a $2.3 million upgrade to an existing intermodal facility near the downtown area, according to the filing.

The new facility would be for automobiles shipped by rail and awaiting delivery to dealerships, and will be built at the San Vel property off Willow Road near Spectacle Pond. Its value was not available by press time.

The proposed company needs approval from the Surface Transportation Board before beginning work. That’s expected to take four to eight months, according to Norfolk Southern spokesman Rudy Husband, who referred further comment to the filing.

“We’re letting the application speak for itself,” he said.

The town has already installed monitoring wells around the San Vel area in anticipation of the new facility.

The town tried to prevent construction of a parking facility in the late 1990s, but Pan Am — then known as Guilford Transportation Systems Inc. — won a court battle after arguing that interstate commerce laws supersede local ordinances.

In May 2003, the town dropped its court appeals, and Guilford agreed to give a 60-day warning and follow Title V regulations for wastewater.

“But they don’t have to comply with any of our recommendations or suggestions,” said Development and Planning Director Christopher Ryan. “Apparently, they are exempt from that process.”

Officials are concerned that the number of cars could create the potential for accidents, including fuel leaks, that could contaminate the drinking water.

“I don’t think we have much of a choice,” said Selectman Cornelius “Connie” Sullivan. “If I had my magic wand, would I prefer they build somewhere else? Absolutely.”

The town has no apparent legal recourse left to prevent construction, added Selectman Rick Gilles.

Board Chairman Carolyn McCreary lamented that Pan Am doesn’t use an existing facility near the proposed San Vel site owned by Pan Am. That site, however, is under lease until 2017 to a rival rail provider, CSX Corp.

“The Surface Transportation Board needs to step in and somehow make them use their own site,” said McCreary. “I don’t know how these things work, but it’s a crime to pave more surface down there by our wells.”

A Middlesex County grand jury indicted Pan Am Railways on April 1 for two counts of not reporting a diesel spill of more than 900 gallons at its rail yard to the Department of Environmental Protection in August 2006.

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