BRUNSWICK, Maine — Opponents of a proposed 60,000-square-foot layover facility for Amtrak Downeaster passenger trains claimed victory on Tuesday after a superior court justice vacated a stormwater management permit for the project because abutters did not receive proper notification.

In a decision dated July 2, Justice Joyce A. Wheeler determined that although the plaintiffs’ properties are separated from the proposed site of the layover facility by a strip of land owned by the state of Maine, they are still abutters under Maine Department of Environmental Protection rules. Therefore, they were entitled to notice by the Northern New England Passenger Rail Authority, which proposes to build the layover facility passenger rail advocates say is needed to increase the frequency of service to and from Brunswick.

According to the written decision, NNEPRA argued that even if the abutters did not receive the notice required under state rules, they did have actual notice of the application “but chose not to participate in the permitting process.”

The rail authority must now return to the Maine Department of Environmental Protection with a new application for a stormwater management permit before any work on the layover facility can begin, Jessamine Logan, a department spokeswoman, said Tuesday.

The abutters have argued that they will be negatively affected by increased noise, vibrations and emissions from the facility, proposed on tracks between Church Road and Stanwood Street in Brunswick.

NNEPRA executive director Patricia Quinn maintains that the building is designed to reduce noise and pollution by allowing trains to power down during the day.

In a release Tuesday, Bob Morrison, chairman of the Brunswick West Neighborhood Coalition, which opposes construction of the layover facility at the site proposed by NNEPRA, wrote, “We’ve said for a long time that NNEPRA is ignoring the concerns of the residents of our neighborhood where this giant industrial garage is going to be built. Now we have a court ruling that agrees with us. … Simply put, an industrial garage (MLF) of this magnitude with the inherent safety, noise, vibration and other unavoidable environmental impacts does not belong in any residential neighborhood.”

According to the release, Brunswick West continues to question NNEPRA’s claims that local zoning and siting laws don’t apply because federal guidelines exempt the rail project from local regulations.

They also wonder if the invalidated permit will affect a decision by the Federal Rail Administration that the proposed facility would have “no foreseeable significant impact on the quality of the human or natural environment.”

Left unsettled by the decision is the question of why NNEPRA has claimed that state and local zoning and siting laws don’t apply because it has federal “pre-emption” status, but applied for a stormwater permit from the state anyway. The size of the proposed rail facility is three times larger than what local zoning laws allow.

Quinn, representing NNEPRA, did not immediately return a call for comment on Tuesday.