The Brookhaven Rail Terminal was fined $500,000 by the state Tuesday for causing or allowing the dumping of construction debris at its facility in Yaphank.

The total fine imposed by the state Department of Environmental Conservation would be reduced to $150,000 if the terminal complies with the terms of a consent decree that its operators signed with the DEC and the Town of Brookhaven. The decree calls for state-supervised removal of the material.

The state agency said it found five piles of questionable debris at the terminal, and two of the piles contained elevated levels of pesticides and other compounds that would require they be disposed of at a site off Long Island.

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Two other piles can be disposed of locally, and one pile requires further testing but could be used for grading or construction at the terminal if contaminated material is not found, the DEC said.

Terminal spokeswoman Judy White said it was "pleased" with the consent decree. "We have agreed to remediate the site, and we will take the steps we need to take. This clears up any environmental issues in regard to DEC," she said.

Robert Calica, a Garden City attorney retained by the town, said it was satisfied with the decree. "The town is relieved that they have been ordered to remove the hazardous material from the site. That was what we wanted originally," Calica said.

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The town had argued that the dumped material was what would normally be found in landfills, and that piles of it had been moved around by the terminal operators as they graded the site and excavated sand. A federal judge found the sand-mining illegal last year and ordered it halted.

The town had also pressed for removal of the material because it feared runoff from heavy rains could leach any contaminants into the aquifer that supplies much of the Island's drinking water.

The Suffolk County district attorney's office has acknowledged it was looking into a referral from the DEC about dumping at the site, but it declined to comment Tuesday.

The consent decree said the terminal operators told DEC staff that they found the dumped material in 2012, the year after its opening on the formerly vacant site. The original 28-acre site was graded since then, "making it impossible to know the nature of site conditions in 2012," the consent decree said.

Nonetheless, the ongoing storage of the material at the site "embodies the operation of a Solid Waste Management Facility," which the terminal did not have a permit to operate, the consent decree said.

The terminal, which waived its right to appeal, agreed to a schedule of disposal for the material that will depend on when DEC approves each step. For example, at least 5,000 cubic yards must be disposed of within 20 days of getting DEC approval for the disposal site. No timetable was given for gaining such approval.