Federal regulators’ rejection of a plea from herring fishermen Thursday could lead to a shortage of lobster bait this fall, critics of the decision said.

The New England Fishery Management Council, meeting in Portland, voted 10-0 against an emergency request to increase the amount of haddock that herring fishermen can catch incidentally on Georges Bank.

The regulators said haddock is too valuable to New England’s struggling groundfishermen to allow herring trawlers to catch more than the 179 metric tons they will be allowed in the year from May 1 to April 30, 2015.

“That’s their lifeboat,” said Thomas Dempsey, a council member from Massachusetts.

Herring fishermen have already caught about 5 percent of their cap, and with the heavy summer fishing season ahead, representatives of the industry said most of the region’s herring fleet could be sidelined as early as September.

That would remove 7,700 metric tons of herring from the market in September alone, said Mary Beth Tooley, a lobbyist for the Rockland-based O’Hara Corp., which owns two herring vessels.

Herring is the primary bait for Maine’s $364 million lobster fishery. “If we run out of bait in September or October, this will be devastating,” said David Cousens, president of the Maine Lobstermen’s Association.

Georges Bank, a productive fishing ground off the coast of Massachusetts, is the source of the vast majority of lobster bait used by Maine’s 6,000 licensed lobster fishermen in late summer.

Herring fishermen are struggling to avoid haddock because the stock on Georges Bank is increasing, said Tooley, who also is a council member but recused herself from Thursday’s vote. At the same time, federal regulators have lowered the cap for haddock bycatch from previous years, she said.

“The biomass has gone up and the cap has gone down. That’s the problem,” she said.

Herring fishermen exceeded their limits of 273 metric tons of haddock last year and 286 metric tons in the previous year.

The regulatory system sets up herring fishermen to fail, said Jeff Kaelin, a lobbyist from Lund’s Fisheries, based in Cape May, New Jersey. “It’s unfair,” he said.

About 100,000 metric tons of herring are caught annually off New England. The fishery in Maine was valued last year at about $16 million, 3 percent of the state’s $531 million commercial fishery, according to the Maine Department of Marine Resources.

Beyond the lobster industry, herring fishermen have few allies. Herring is forage food for many marine mammals, birds, and larger fish like tuna and striped bass. Conservation groups have sought for years to limit the catch of herring trawlers, the largest fishing vessels in New England.

Over the past two years, bycatch from those trawlers accounted for more than 10 percent of all the haddock caught off New England, said Greg Wells, a senior associate with The Pew Charitable Trusts.

About 570 people signed a letter to the council urging it to vote against any expansion of the bycatch allowed for the herring trawlers.

Roger Fleming, a member of the Herring Alliance, composed of 90 groups along the East Coast, said the herring fleet has a “pattern” of seeking exemptions whenever it approaches a cap on bycatch. “That’s not the way accountability measures are supposed to work,” he said.

Fleming said that fears of a lobster bait shortage are overstated. “The market tends to take care of that issue,” he said.

Besides fresh herring, lobstermen use frozen herring and other fish from around the world for bait, but those alternatives are more expensive.