Under a compromise endorsed Thursday by the New England Fishery Management Council, the scalloping sector of the region’s fishing fleets would give the groundfishing fleet a big chunk of its allocation for Georges Bank yellowtail flounder.

The handoff to groundfishermen landing the catches in Gloucester from scallopers working primarily from New Bedford would boost the yellowtail allocation for groundfishing boats by about 70 percent, the Associated Press reported. It would also ease the potential for yellowtail hauled up as groundfishermen’s bycatch from choking off fishermen’s ability to land other fish.

In exchange, the scallopers would be indemnified for exceeding their voluntarily reduced allocation of yellowtail this year.

The arrangement, debated at length Thursday at the council’s June meeting in Portland, Maine, must be approved by NOAA, but it was brokered by Sam Rauch, who has been the acting administrator of NOAA’s National Marine Fishery Service.

The deal was not unanimously supported. Environmental interests objected to the indemnification of the scalloping fleet if it exceeds its allocation of 307 metric tons of yellowtail.

The deal attempts to make the best of an increasingly discouraging portrait of the vitality of the yellowtail flounder stocks on Georges Bank, the biggest of the banks in the Northwest Atlantic; Georges rises between the Canadian Maritime coast to southeast of Cape Ann, about 100 miles east of Cape Cod, and historically has been one of the most productive grounds in the ocean.

Both nations have worked Georges for centuries.

Rauch, council staff, industry and government drew from a major workshop in New Bedford organized in May soon after a stock assessment found yellowtail so weakened that an 80 percent cut in catch limits was issued.

Rauch used a similar approach to making the best of another shock of bad news earlier this year — the benchmark Gulf of Maine cod assessment that contradicted a 3-year-old study of inshore cod. Using his emergency powers, Rauch managed to limit the 2012 reduction in cod stocks to 22 percent, when many feared steeper cuts.

Under the terms of the deal endorsed in Portland, the scalloping sector transfers to the groundfishing fleet the best part of its allocation of yellowtail — about 200 metric tons — so that yellowtail will not become a “choke” species and prevent the boats from fishing for anything for fear of hauling up yellowtail as bycatch.

Scallopers would keep 156.9 metric tons of yellowtail for their bycatch.

The second part of the compromise involves the indemnification of the scallopers from any penalty should they exceed their reduced allocation of yellowtail as bycatch.

The hard catch limits and penalties for exceeding the catch limits were written into the 2006 reauthorization of the Magnuson-Stevens Fishery Conservation and Management Act.

Waiving the accountability element of the law would be a first, and an unpopular one with conservation interests. Representatives of Oceana, the Conservation Law Foundation, who are not on the council, and the Nature Conservancy’s Sally McGee, who is, all protested the free ride given scallopers as part of the compromise.

Drew Minkiewicz of the Fishermen’s Survival Fund, an industry group representing scalloping interests, conceded that the council and the scallopers were taking a “drastic step,” but said the impulse to get both fisheries “to maximize” output justified the action.

The scalloping fleet has been making progress in reducing its bycatch of yellowtail both with gear innovations and communications that warn scallop boats away from beds found to have concentrations of yellowtail. The fleet caught fewer than 100 metric tons of yellowtail last year, Minkiewicz said in a telephone interview.

He also credited Rauch with the knack of galvanizing competing interests into common interests.

“You came up with a good solution, Sam,” agreed Vito Giacalone, policy director of the Gloucester-based Northeast Seafood Coalition, president of the Gloucester Community Fishing Preservation Fund and an active fisherman. “This is problem solving.”

But behind the expressions of relief was a widespread concern for signs of a downward spiral in the vitality of the Georges Bank ecosystem.

“I have big concerns,” Ron Smolowitz, also of the Fishermen’s Survival Fund, told the council. “There’s something significant going on out there independent of the fishery.

“Some people believe the (stock) survey is at fault; that’s not the problem,” he said. “There’s a fishery without large fish, fish are underweight and not replacing (themselves). Something is wrong with the fish that (has) nothing to do with fishing.”

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