A Cumberland County Superior Court justice has thrown out a stormwater management permit issued for a proposed Brunswick train maintenance facility, saying neighbors weren’t properly notified of the application for the permit.

Last week’s ruling by Justice Joyce A. Wheeler means the Northern New England Passenger Rail Authority will need to re-apply for the permit and, presumably, neighbors will have a chance to comment on whether the stormwater management permit should be issued.

NNEPRA, which operates The Downeaster passenger trains between Maine and Boston, wants to build a $16 million layover facility in Brunswick, where trains can be serviced overnight before resuming their runs.

Neighbors have fought the proposal, saying the site isn’t appropriate in what is otherwise a residential neighborhood. The neighbors call the facility “a giant industrial garage” that would create safety, noise and vibration issues.

Wheeler said NNEPRA and the Maine Department of Environmental Protection had determined that the neighbors did not have to be alerted about the permit application because a strip of state-owned lands lies between the site for the facility and the neighbors’ properties.

Wheeler said the DEP’s own rules define an abutter as someone who owns land that either adjoins a project site or is within a mile of the project boundary, “including owners of property directly across a public or private right of way.”

Wheeler said the rule is “intended to protect those property owners whose property is close to and most impacted by a proposed project, but happens to be separated by a road or similar right of way,”

Wheeler’s ruling did not deal with NNEPRA’s contention that it has federal “pre-emption” status and isn’t subject to state and local zoning laws.

“Apparently, NNEPRA believes it can pick and choose which laws it wants to comply with,” said Bob Morrison, chair of the Brunswick West Neighborhood Coalition.