BRUNSWICK, Maine — Plans to build a layover facility in Brunswick for Amtrak passenger trains suffered another setback Wednesday as Patricia Aho, commissioner of the Maine Department of Environmental Protection, fired off a six-page letter that asked the project’s backers to answer almost two dozen questions.

Aho’s letter comes two months after a Maine Superior Court judge threw out a stormwater management permit for the proposed 60,000-square-foot train layover facility between Church Road and Stanwood Street. Also on Wednesday, the Maine Department of Environmental Protection told rail officials that a new application for the permit was unacceptable and demanded significant new information about the proposed project.

In her letter, Aho also directed the Northern New England Passenger Rail Authority — which proposed the controversial project as an essential component to its expansion of passenger rail to Brunswick — to address all correspondence about the project directly to her office.

“These are the types of things we’ve been clamoring for for years,” said Bob Morrison, chairman of the Brunswick West Neighborhood Coalition, which opposes construction of the facility at its proposed site. Morrison said the department’s communication with NNEPRA on Wednesday was powerful, and indicative that the neighbors’ concerns are finally being heard and addressed.

But NNEPRA executive director Patricia Quinn said Wednesday evening that much of the information Aho requested is readily available, and NNEPRA is eager to provide any answers the state requests.

NNEPRA, which operates the Downeaster for Amtrak, has faced mounting opposition from the neighborhood group, which says people who live near the proposed structure will be harmed by increased noise, vibrations and emissions from the facility.

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

In her letter Wednesday to Quinn, Aho included a 21-bullet list of items about which she requires additional information.

Among them, she asked Quinn to submit plans to address soil management, on-site chemicals and septic pump-out. She asked about a plan for hydrogeologic testing of the aquifer, a plan to store and handle 55-gallon oil storage tanks on site and information about whether the Brunswick wastewater treatment plant could handle effluent from the proposed facility.

Further, Aho asked how NNEPRA proposes to ensure that stormwater runoff is acceptable, given elevated concentrations of lead and arsenic, among other metals, found on the proposed site that will leach into the water.

Aho also wrote that during a July 30 meeting with state environmental officials, neighbors of the proposed site alerted them to a private drinking water supply well “in far closer proximity to the proposed facility than the 0.5 mile stated” previously by NNEPRA.

“The department is concerned other nearby residences have private wells, relying upon the groundwater in the aquifer underlying the rail yard for their drinking water,” Aho wrote. “The department asks how NNEPRA will ensure private drinking water supply wells located in close proximity of the rail yard are not at risk from existing or future contaminated groundwater?”

The commissioner asked for a plan to establish how long engines will idle at the entrance of the facility, and asked that NNEPRA voluntarily agree to implement noise limits consistent with the standards set forth in state rules.

Aho’s letter was penned the same day her department ruled a new application for a stormwater management permit incomplete.

Bill Bullard, project manager for the DEP’s Division of Land Resources Regulation, wrote to the Northern New England Passenger Rail Authority that the new application was missing a number of required elements, including a dewatering plan for construction of the stormwater and sanitary sewer systems and a plan showing the location of erosion control best practices.

A page from the water quality treatment plan also was missing, as were other calculations and a table, and the legend appeared to be incomplete or in conflict with the plan, according to Bullard’s letter.

On July 2, Superior Court Justice Joyce A. Wheeler vacated a stormwater management permit for the facility after determining that abutters of the project had not received proper notification.

Quinn said Wednesday that the letter deeming the application unacceptable was “disappointing and surprising.” Several items were included on a separate page or had been left out during printing, she said.

NNEPRA already has replied to the DEP, requesting that any corrections and new information be allowed to amend the original application, rather than requiring NNEPRA to start all over again.

“We felt that most things outlined in the letter were mostly administrative-type requests that would be resolved through due process,” Quinn said.

Quinn said she had only “skimmed” Aho’s six-page letter, but said it seemed to address “a lot of ongoing discussions we’ve been having with the DEP on a number of issues.”

Some of the requested information is not required of an applicant but NNEPRA will provide it “to make sure they’re comfortable with the results and with the impact of the facility,” according to Quinn.

Nicole Vinal, who lives on Hennessey Drive in Brunswick, near the proposed facility, said Wednesday that the DEP decision was a victory in the Brunswick Neighbors’ effort to force thoughtful evaluation of the proposed project.

“All along, this has been a sort of hasty attempt to throw this mammoth building in our backyard,” Vinal said. “They need to examine these buildings appropriately… if it’s built, it needs to be completely evaluated and done properly.”

“There’s no question that this process has been scrutinized to the nth degree,” Quinn said. “It’s a highly controversial project and we want to make sure nothing is missed and we haven’t made any mistakes. But I don’t think that necessarily takes away from the merits of the project at all. Like with anything else, a bunch of experts sit down and review a project and a lot of ideas come up. I think we’ve done a lot of work, we’ve got a good team, and I don’t think there’s anything [in the letter] that really questioned the viability of the project. There are just things that need to be looked at and questions that need to be answered, and we’re happy to do that.”

Because federal rail regulations supersede most state and local authority, opponents of the project previously have been frustrated when seeking recourse from Brunswick town government or the state. However, in March, Aho’s boss, Gov. Paul LePage, entered the controversy over the proposed facility by writing a letter to federal rail officials demanding scrutiny of the proposal.

A phone call to the DEP on Wednesday was not returned.