A government agency tasked with regulating commercial fishing in Hawaiian waters wants to let longliners ensnare twice as many endangered sea turtles.

Armed with a new biological study, the National Marine Fisheries Service is seeking public input over the next few weeks on a pair of rules that would ease restrictions on the swordfish industry.

The official notices were posted Monday, but environmental groups started gearing up months ago for what will be the latest challenge in a decade-old fight over how many leatherback and loggerhead turtles fishermen can accidentally kill or catch each year.

Both species have been protected under the Endangered Species Act since 1973. Hawaii’s longline-fishing industry was catching hundreds and killing dozens of turtles every year in the 1990s until strict management measures were imposed — reducing the impact by more than 90 percent, according to federal documents.

The current allowed human “interactions,” such as fishing gear entanglements or incidental hooking, with loggerheads is 17 and with leatherbacks is 16. NMFS proposes upping these limits to 34 and 26, respectively.

The last time NMFS tried to increase these limits, environmental groups took the agency to court and were successful in keeping the current caps. It looks likely that this latest effort will wind up before a judge again.

“We have an obligation to conduct fishing here in the islands in a responsible way and I think that we can do that. The history here reflects that we can make sure we have fish on the table and fish in the sea,” Earth Justice attorney David Henkin said Monday. “We should not allow the drive of a very small group of people who want to make more money to undermine our decisions so that these species who have roamed for millennia can continue to do that.”

The Western Pacific Regional Fishery Management Council, which advises NMFS, maintains that the latest science shows increasing the limits would not hurt the turtles’ recovery progress, said Paul Dalzell, a senior scientist for the council.

“We manage to maintain low impacts on turtle populations,” he said, noting the council has been at the forefront worldwide in implementing precautionary measures like circle hooks and different kind of fish bait that turtles don’t like. “The science is detailed, explicitly laid out, and deemed not to jeopardize the continuity of the population.”

Dalzell said he expects NMFS will consider the public input, but likely approve the final rule unchanged based on its 162-page biological opinion issued Jan. 30.

“We will be commenting and providing peer review and hopefully convince them that they’ve been taken along for a ride,” Henkin said, but added that there’s a “good chance” the matter will end up back in court.

NMFS’ biological opinions have been at the root of lawsuits environmental groups have filed in recent years.

Earth Justice attorney Paul Achitoff represented Turtle Island Restoration Network, the Center for Biological Diversity and Kahea: The Hawaiian-Environmental Alliance against NMFS in a case filed in 2009. The groups challenged a 2008 biological opinion on which NMFS based its recommendation to increase the loggerhead interaction cap from 17 to 46.

In January 2011, the federal court ordered NMFS to do another biological opinion for the shallow-set fishery, where longline fishermen hunt swordfish. This time around, however, NMFS had to include in the study any projected impacts from climate change, such as sea-level rise or warmer ocean waters.

NMFS appealed the district court’s ruling, but the decision was upheld in March of this year.

Henkin faulted the agency’s “head-in-the-sand attitude” in the 2012 biological opinion that simultaneously acknowledges long-term inevitable factors while saying everything looks fine based on the modeling’s 25-year outlook.

Dalzell said environmental groups may object just on principal if a single turtle is harmed, but the Endangered Species Act allows for a limited number of human interactions.

He said the agency has more information than ever about the endangered turtles — such as evidence of healthy nesting areas in Japan and Indonesia — and can therefore be more confident in revising the limits.

When the longline industry impacted the turtles to the point that the fishery was shut down from 2001 to 2004, Dalzell said the council took the position that rather than just be a bystander they had to get actively involved in management plans.

This decision, he said, led to the new science for better bait, safer hooks and conservation measures to help save the turtles.

The fishery was closed again at the beginning of the 2006 season for loggerheads and last year for leatherbacks, Dalzell said. But those are the only times the industry has reached the current caps on interactions with the species since 2004.

Henkin questioned why the agency wants to increase the current court-imposed limits since it has rarely reached them over the past several years.

In September 2011, the U.S. Fish and Wildlife Service and National Oceanic and Atmospheric Administration, which NMFS falls under, determined that the leatherbacks and loggerheads should remain on the endangered species list despite positive population trends. Leatherbacks are classified as endangered and loggerheads as threatened.

The agencies at the time cast aside the claim that more turtles are killed when Hawaii-based longline fisheries don’t meet the market demand and foreign fleets sail into the high seas to fill it. The feds acknowledged that efforts by Hawaii fisheries to minimize loggerhead deaths and injuries have been substantial and effective, but the population remains substantially below historic levels.

Unlimited Swordfish?

Dalzell said the swordfish population is thriving and there is still a “huge demand,” primarily from people on the East Coast of the United States.

Another proposed rule that NMFS posted for public comment Monday recommends increasing the limits on the number of swordfish that fishermen can catch in certain areas.

While longline fishermen primarily hunt swordfish in shallower waters, sometimes they will catch them when they are deep-sea fishing for ahi. The current 10-swordfish limit on any deep-set trip has resulted in waste, according to NMFS.

“The fishermen assert that, because swordfish stocks are healthy and are not subject to overfishing or approaching an overfished condition, the regulatory discards amount to wasted opportunities to sell the excess fish,” NMFS says in its statement on the proposed rule. “The lost opportunities result in lost wages to fishermen and a reduction of the fish supply to seafood consumers.”

Based on the council’s recommendation, NMFS proposed allowing unlimited swordfish to be caught each trip if an NMFS observer is aboard the boat. The proposal calls for tighter restrictions without an observer and if circle hooks are not used.

The public comment period for the swordfish rule ends July 2. The comment period on the increased turtle limits ends July 11.