PORTLAND, Maine — Seeking to end a long-running disagreement about exactly how many cod are left in the Gulf of Maine, federal scientists plan to outfit commercial fishermen with equipment used to establish groundfish quotas.

The fishermen tend to argue that there are more cod than the government realizes; therefore, the number they may legally catch should be higher. Government scientists counter that fishermen’s natural tendency to fish where they are most likely to catch large numbers leads them to overestimate the cod population in the entire Gulf of Maine.

By next year, the Northeast Fisheries Science Center hopes to begin outfitting commercial boats with surveying equipment and paying fishermen to pull in catches that will supplement the regular trawl surveys conducted by government scientists, according to Russell Brown, who heads the center’s population dynamics branch. The gathered data will be fed into the complex process used to set catch quotas.

It’s a collaboration that Brown hopes will give regulators a more detailed picture of the fish population and build trust among fishermen, who in turn see it as an opportunity to show the scientists what’s really going on.

For years, fishermen and scientists have clashed over how to properly estimate fish populations and set the catch quotas that rule the livelihoods of Maine fishermen. Fishermen suggest that scientists are missing fish and setting the quotas too low, while scientists say fishermen are missing the big picture. But both groups believe collaboration would be a positive step toward better protecting Maine’s fishing industry and environment, even as ocean waters warm.

“It’s really perplexing that you’ve got a set of federal scientists who are sampling the ocean methodically and coming up with a very different picture than the fishermen about what’s going on out in the Gulf of Maine,” Jonathan Labaree of the Gulf of Maine Research Institute said.

Fishing in the Northeast is regulated by a complex quota system. It sets out an overall catch limit that is then broken down by subregion and eventually by fishermen. Different caps are set for different species, based in part on how healthy federal scientists determine the respective populations to be. Exceeding a season’s allocation of one type of fish can mean a fisherman must stop catching all other types, too — possibly ending their season.

And some fishermen say the current cod quota underrepresents a species they believe is doing better than it was a decade ago, despite warming waters, and wreaks havoc on their ability to catch other fish.

“We try to avoid [cod] at all costs,” Brian Pearce, who fishes for pollock and white hake out of Portland harbor, said. “The science has to catch up with what’s really out there. … It seems like the stock is rebuilding faster than the government believes it is.”

Brown said the number of cod fishermen are seeing in the waters off Portland and Gloucester, Massachusetts, isn’t representative of the Gulf of Maine as a whole. Rather, he said, cod are clustered in these areas precisely because there are few remaining in the water off Down East Maine. That’s what cod did off Newfoundland’s Grand Banks soon before that fishery collapsed, he said.

Bert Jongerden, general manager of the Portland Fish Exchange, thinks this theory is misguided.

He and others in the industry say the real problem is that the scientists are fishing wrong. They claim that the type of trawl net scientists use and the boat they pull it from, which is larger than many commercial fishing vessels, do a poor job catching certain species. Pearce claimed that the surveys happen in the wrong places and that because the ocean has warmed, cod cluster in deeper water than they used to.

Brown agreed that there are places where the larger science vessel can’t navigate and that their gear isn’t meant to “maximize the catch of cod or haddock or flounder” but added that their goals are different from those of commercial fishermen.

He hopes that having commercial vessels gathering data as part of the same peer-reviewed process that his organization uses to survey fish will round out what is known about fisheries in the Gulf of Maine. But Brown also emphasized that the fishermen are mostly seeing the places where there are a lot of fish — he’s worried about the places where there aren’t.

“We’re trying to manage these stocks so we can maintain profitable fishing ports in places like Portland, Maine,” he said.