Brookhaven Town officials have called on the state to scrap plans to cap a contaminated Long Island Rail Road yard in Yaphank and instead remove soil from the property.

Supervisor Edward P. Romaine, in a letter to the state Department of Environmental Conservation, said the proposal to cap the 4-acre site near River Road was "completely unacceptable" because studies have found pollutants such as zinc, arsenic, lead and copper on the parcel.

The LIRR used the site as an unauthorized dump for three decades before it was closed in the 1970s, the DEC said. The DEC plans to cover parts of the property with soil, stone or concrete, and an asphalt cap would be built on an adjoining property. The plan also calls for removing contaminated fill from an adjacent, undeveloped residential property, and replacing it with clean fill.

Those plans could upend town efforts to conserve the Carmans River, which runs less than 500 feet from the Yaphank site, Romaine said in the letter to the DEC, a copy of which was furnished by his office to Newsday.

"The health of our residents and our tremendous investment in the ecologically fragile Carmans River must be permanently protected from the impacts of the contaminants at this site," Romaine wrote.

The DEC, in a statement, acknowledged receiving Romaine's letter, but offered no comment on it.

The Metropolitan Transportation Authority has agreed to pay up to $9 million for the cleanup, spokesman Sal Arena said in an email. MTA officials "will be carefully reviewing the supervisor's letter as well as consulting further" with the DEC, he said.

Councilwoman Connie Kepert, who represents the area, said capping the site would not protect nearby homes.

"They really do need some more effective way of excavating that contamination," she said.

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Adrienne Esposito, executive director of Citizens Campaign for the Environment, which has an office in Farmingdale, said capping similar polluted sites has proved to be ineffective.

"It's just a remedy riddled with potential failures," she said.

Civic leader MaryAnn Johnston of Yaphank said the DEC proposal is "really depressing," adding: "We're spending a fortune to conserve the river, and the railroad proposes that we just cap and bury? It's not going to work."

The East Yaphank Civic Association will host a public discussion of the cleanup plan at 7:30 p.m. Thursday at Dowling College's Brookhaven campus, 1300 William Floyd Pkwy., Shirley.