Emergency restrictions aimed at protecting plummeting cod stocks, set to go into effect Thursday in the Gulf of Maine, have some fishermen complaining that one group that routinely kills cod won’t be affected by the new rules – the region’s lobstermen.

In 2008, the year for which the most recent data are available, an estimated 177,000 codfish were captured in lobster traps in state waters off Maine.

Fishing boats with gill nets and trawl gear are banned from coastal waters where cod stocks gather and spawn, but lobster boats face none of those restrictions. Moreover, none of the data about cod mortality in the lobster fishery is included in population projections used to set fishing regulations for cod.

Allyson Jordan, a Portland fisherman who operates two groundfishing boats, said regulators will have a hard time rebuilding cod stocks if they only impose restrictions on New England’s struggling groundfish fleet and ignore the much larger lobster fishery.

“It’s not fair,” she said. “If everybody else is allowed into the closed areas, you will not be effective in protecting the spawning grounds.”

The cod stock in the Gulf of Maine is now at 3 percent to 4 percent of the level deemed sustainable, according to scientists. With the population so low, there is a new focus among federal biologists to understand all the environmental factors that could be affecting cod stocks. That includes the 3 million lobster traps in Maine waters, plus the traps off the coasts of New Hampshire and Massachusetts, said Paul Rago, chief of the population dynamics branch for the National Marine Fisheries Service at the Northeast Fisheries Science Center in Woods Hole, Massachusetts.

“It is clearly something everyone is now focused on, and appropriately so, with the limits as low as they are,” he said.

The new restrictions on the groundfish fleet impose “rolling closures” on coastal fishing grounds where cod are most abundant and where they spawn. Those areas are generally located between Cape Ann, Massachusetts, and the coast of New Hampshire. Fishing boats are not allowed to use gill nets or trawl nets in those areas.

In addition, boats outside those areas can now catch only 200 pounds of cod per fishing trip, a measure intended to limit the incidental cod catch when fishermen pursue other groundfish stocks, such as haddock, hake and redfish. The new measures do not apply to fishing on Georges Bank, where the cod stock is larger.

Understanding the impact of the lobster industry on cod mortality is important for getting an accurate assessment of the size and health of cod stocks, Rago said. However, using that knowledge to regulate the lobster industry is unlikely because of jurisdictional issues, he said. The lobster fishery is mostly in state waters and regulated by state governments, while groundfish are regulated by the federal government.

When assessing cod stocks in the Gulf of Maine, Rago said, federal regulators don’t take into account the impact of the lobster industry on cod because there is no reliable data. He said scientists know that cod is among the top species captured in lobster traps, but they don’t know the extent of the problem, and they also don’t know what fishermen do with the cod that are captured.

He said scientists don’t even know whether cod can survive the trauma of being caught in a trap and brought to the surface. When a codfish is quickly brought to the surface, its swim bladder often ruptures as gas in the bladder expands.

The only available data on the issue was compiled by Carl Wilson, a biologist with the Maine Department of Marine Resources who used figures compiled over a three-year period in which three trips a month were taken in each of the state’s seven lobster zones.

The survey concluded that cod was the fifth-most-common fish caught in traps. Sculpin longhorn was tops, followed by sea raven, sculpin shorthorn and cunner. Based on the 317 cod found in traps from 2006 to 2008, he estimated that 177,247 cod were caught in lobster traps in Maine in 2008.

However, that estimate does not fully account for the variability of bycatch in the lobster fishery in different parts of the coast and in different seasons, said Jeff Nichols, a spokesman for the department.

He said the department is aware that the groundfish industry and the New England Fishery Management Council are concerned about this issue, and DMR staff is analyzing the department’s sea sampling data over the past five years to provide a more accurate picture of what is happening.

Meanwhile, Yong Chen, a fisheries scientist at the University of Maine, recently began studying the survival rates of cod and cusk after they are captured in lobster traps. He also plans to survey lobstermen to find what they do with captured cod.

So far, he has found that most cusk survive the trauma, and he suspects he also will find high survival rates next year when he studies cod. Three of his students working on the project met Wednesday with Rago and other officials at the Northeast Fisheries Science Center to discuss ways to collaborate and share data.

Chen said cod get caught in traps when they try to eat the bait.

Maine groundfishermen and lobstermen have battled each other for years.

Groundfish boats sometimes sweep up lobsters in their nets as bycatch, angering lobstermen who believe the draggers are catching lobsters on purpose. Groundfishermen have sought to change Maine law so they can sell those lobsters, but the politically powerful lobster fishery, which last year accounted for $364 million of the $531 million brought in by Maine’s fishing industry, easily crushed those attempts. There are roughly 50 groundfish licenses issued in Maine compared with 6,000 lobster licenses.

Patrice McCarron, executive director of the Maine Lobstermen’s Association, said it is “rare incidence” for lobstermen to encounter cod in traps. She said it’s illegal for a lobsterman to land a cod and that most lobstermen throw them back into the ocean alive because they want to see the stock rebound.

“People are well aware of the struggles of the groundfish industry,” she said. “I do think there is a real respect for people who earn their living from the sea.”

But Bert Jongerden, general manager of the Portland Fish Exchange, suspects there is a different outcome for most codfish unlucky enough to end up in a trap. He said lobstermen will kill the cod and either use it as free lobster bait or take it home for supper.

“They are not going to pat the codfish on the head and let it go,” he said.