While some spawning areas are closed to trawling and gill-netting, lobster traps would still be allowed.

Federal regulators voted Wednesday to exempt the lobster fishery from measures aimed at saving plummeting cod stocks in the Gulf of Maine.

The vote to protect the lobster fishery came as the New England Fishery Management Council endorsed some of the toughest regulations the region’s groundfishermen have ever seen.

Meeting in Newport, Rhode Island, the fishery council voted to close some important coastal fishing grounds to protect spawning cod stocks for the fishing season that begins on May 1. Similar closures are already in effect under an emergency measure that will expire in six months.

The closed areas are generally on fishing grounds between Massachusetts Bay and southern Maine.

Recreational fishermen would be allowed to fish in the closed areas but would have to throw back any cod they catch. The council also decided that mid-water herring trawlers would not be subject to the measure.

The council’s recommendations now go to the National Oceanic and Atmospheric Administration, which has the final say.

The issue of cod bycatch by lobstermen drew a lot of attention because it was the first time the lobster fishery was drawn into the debate over how to save the region’s cod stock, which has fallen to an all-time low – 3 to 4 percent of the level deemed sustainable.

Groundfishermen complained that it’s not fair to allow lobstermen to set traps in the closed areas because small cod enter traps to feed on bait.

In 2008, the year for which the most recent data are available, an estimated 177,000 cod were captured in lobster traps in Maine waters. If each fish weighed a pound, the cod bycatch would total 80 metric tons – 13 percent of the total commercial cod catch in Maine that year.

Ultimately, the council voted 14-1 to reject a recommendation to ban lobster gear in the closed areas. That means lobstermen would be allowed to set traps in areas where groundfish trawls and gill nets are prohibited.

“There is no definitive evidence right now to support prohibiting lobster pot fishing in closed areas,” said Patricia Fiorelli, spokeswoman for the council.

Allyson Jordan, who lives in Portland and operates two draggers out of Portland Harbor, said she is disappointed by the vote.

“They will shut down even more ground to us but not anybody else,” she said. “It doesn’t make any sense.”

One consolation, she said, is that the issue is now “on the radar” of federal regulators, so the council will take up the issue again if more evidence emerges that the lobster fishery is hurting the cod population’s ability to rebound.

Patrick Keliher, commissioner of the Maine Department of Marine Resources, said he was pleased by the council’s decision.

He said the 2008 data is a rough estimate that has no place in discussions about management measures.

He said he is also pleased that the council addressed jurisdictional issues on Wednesday by ensuring involvement of the Atlantic States Marine Fisheries Commission in the data analysis and ongoing management discussions.

That commission regulates the lobster fishery in federal waters.

“I will continue to support efforts to acquire and analyze appropriate data to ensure that a thorough assessment of cod bycatch in the lobster fishery occurs,” he said.

In a letter to the council, Patrice McCarron, executive director of the Maine Lobstermen’s Association, criticized the science used to characterize the level of cod bycatch by lobstermen. She also said there is no peer-reviewed research on the impact of the bycatch on the recovery of the cod population.

The council voted late Wednesday to essentially continue the current emergency restrictions through next year’s fishing season. However, the council made some changes in the location and size of the areas, to make it easier for fishermen to catch healthy fish species, such as haddock.

Ben Martens, executive director of the Maine Coast Fishermen’s Association, which represents 35 boats, said Maine fishermen benefit from the change because Platts Bank, a productive fishing ground off the Maine coast, would stay open to fishing in July and August, a time of year when fish usually are plentiful. Under the emergency measure, he said, the area would have been closed.