The National Marine Fisheries Service violated the Endangered Species Act by not properly reporting the lobster industry’s harmful impacts on the North Atlantic right whale, which it knew to be more than three times what the dwindling species could sustain, according to a federal judge.

In a ruling issued Thursday, U.S. District Judge James Boasberg accused the service of failing to follow the letter of the landmark environmental law because it would have meant the fishery, which rakes in millions of lobster and dollars each year, would not be able to proceed.

“The service and the statute pass each other like ships in the night,” Boasberg wrote in his 20-page ruling.

The decision caught the Maine Department of Marine Resources, which regulates Maine’s $485 million-a-year lobster fishery, and the Maine Lobstermen’s Association, the industry’s largest trade association, off guard. Both agency and association officials said they needed time to digest the ruling before commenting.

“Upon an initial review, this is a deeply disappointing decision,” Gov. Janet Mills said Thursday night.

Marine Resources Commissioner Patrick Keliher is leading the state’s efforts to keep its most valuable fishery alive in the face of the service’s latest review of how the lobster industry impacts right whales. Boasberg is presiding over a lawsuit brought by four environmental groups that argue that the service’s 2014 authorization was illegal.

The service is set to issue a draft regulation in July that will outline new right whale protections that U.S. lobstermen must adopt, which could range from seasonal area closures like the one enacted in 2014 in Cape Cod Bay, to a mix of trap reductions and more traps per buoy line as recommended by a whale task force.

Maine came up with a right whale protection plan of its own, but federal regulators say it fell short.

Defenders of Wildlife, one of the environmental groups that sued the service over its authorization of the lobster industry, welcomed the timely ruling, which comes at the end of a calving season that saw only 10 new right whales – a third of what is needed to keep pace with deaths  – and the looming new federal rule.

“We’re pleased with the ruling, not just because of where the judge found the agency violated the law, but also what he had to say about our other concerns,” senior attorney Jane Davenport said. “He put them on notice that they had better follow every part of the Endangered Species Act.”

Davenport said she believes the lobstering industry and the right whale can coexist if both regulators and industry embrace new technology, including ropeless fishing. Even with ropes, however, the service could be urging the industry to do more, she said. She hopes this ruling will speed that up.

Under federal law, the service is required to file what is called an incidental take statement if it concludes that any projects or programs it funds or permits would have more than a negligible impact on an endangered species like the North Atlantic right whale, which now number about 400.

In its 2014 authorization of the U.S. lobster fishery, however, the National Marine Fisheries Service failed to file such a statement even though it concluded that the fishery had the potential to seriously injure or kill an average of 3.25 whales a year as a result of entanglements in surface-to-seabed buoy lines.

Scientists believe the species, which was once hunted nearly to extinction for its blubber, cannot survive if even one whale dies a year in U.S. waters, whether that be from entanglement in fishing lines or gillnets or from blunt trauma caused by ship collisions.

Instead, the service established numerical triggers when authorizing the lobster industry that, if surpassed, would require it to reconsider new lobster fishing rules. The service believed that to fulfill the intent – if not the letter – of the law, which, if followed exactly, would have prevented authorization of the fishery.

Lawmakers did not intend the service to use the Endangered Species Act to close fisheries, NMFS argued.

But Boasberg cited a U.S. Supreme Court ruling that forced the Tennessee Valley Authority to abandon an already constructed taxpayer-funded dam because it was found in violation of the Endangered Species Act when he concluded that a potential closure is not a reason for violating the law.

“The Service’s failure to include an (incidental take statement) after finding that the American lobster industry had the potential to harm the North Atlantic right whale at more than three times the sustainable rate is about as straightforward a violation of the (Endangered Species Act) as they come,” Boasberg said.

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