Hawaii’s commercial swordfish fleet has been shut down for the rest of the year following a court order aimed at protecting endangered loggerhead sea turtles.

The National Marine Fisheries Service closed the Hawaii shallow-set longline fishery in a move heralded Wednesday by conservation groups that sued for the turtle protections.

“We scored a victory for loggerhead sea turtles,” said Todd Steiner, biologist and executive director of Turtle Island Restoration Network, which joined the Center for Biological Diversity in 2012 to sue the federal agency after it allowed Hawaii-based swordfish longline fishing vessels to double the number of loggerheads they can snag incidentally, or unintentionally, in a year.

The lawsuit was initially thwarted as U.S. District Judge Susan Oki Mollway, without a trial in 2013, upheld the expanded bycatch limit of 34 loggerheads annually.

But the conservation groups, represented by Earthjustice in Honolulu, appealed the ruling.

In a 2-1 split decision in December, the 9th U.S. Circuit Court of Appeals ruled that the National Marine Fisheries Service was arbitrary and capricious in concluding that the North Pacific loggerhead population would not be jeopardized by the higher catch rate.

Since then the parties have been negotiating a settlement, with an agreement approved last week.

Under the court order the swordfish fishery will close, and a new biological assessment will determine what the limit will be next year.

“It’s a good result for all parties,” said Jim Cook, board member with the Hawaii Longline Association.

Cook said the fishery was about to close anyway because the number of loggerheads caught this year was nearing its limit.

Swordfishing represents about 10 percent of the Hawaii longline fishery, worth about $12 million a year. The rest of the 140-boat Honolulu fleet aims to catch bigeye tuna, which are found at deep depths.

Cook, who owns five tuna boats with business partner Sean Martin, said the 34-turtle limit seems about right to him because the swordfish fishery catch has been averaging only about 19 loggerheads over the last five years.

“This was an exceptional year for turtles,” he said.

But Earthjustice attorney Paul Achitoff said the number is not only unacceptable, the industry should be working to modify its fishing methods to eliminate collateral damage.

Achitoff said conservationists were disappointed when the National Marine Fisheries Service raised the loggerhead bycatch limit to 34 from 17 in 2012 shortly after the species was placed on the endangered species list. That prompted the lawsuit.

Swordfish fishermen use squid bait on hooks deployed on long lines in relatively shallow depths. The fishery is notorious for snagging both sea turtles and seabirds.

According to the Western Pacific Fishery Management Council, all swordfish boats are assigned observers to document interactions with protected species, while only 20 percent of the tuna boats, which generally have fewer interactions, have observers.