PORTSMOUTH, N.H. – With their industry in crisis, New England fishermen met with scientists Friday in a forum meant to shed light on, and air disagreement about, the controversial science of counting fish.

Fishermen have long questioned fish population estimates offered by scientists, often because the counts contradict what they find at sea. And with key stocks struggling and huge new limits set to decimate an already limping industry in 2013, the unrest is widespread.

“The fishing industry, in general, is in a very negative mood,” said David Goethel, a New Hampshire fisherman.

In recent months, federal and regional regulators have met with fishermen more often to increase cooperation and try to figure out how to outlast the crisis.

John Bullard, head of the National Oceanic and Atmospheric Administration’s Northeast office, said fishermen and scientists shouldn’t be at odds because both have expertise on fish behavior and are seeking the same “elusive truth.”

“We’re just trying to find ways, big and small, to have increased involvement because that increased involvement is going to increase our understanding,” he said.

At the meeting in Portsmouth on Friday, scientists detailed the complexities and uncertainties of counting fish. They also took questions from fishing industry advocates who are frustrated over what they say are shifting and incorrect population estimates that have led to lower catch limits.

Earlier this year, New England fishermen absorbed a 22 percent cut in the catch of cod in Gulf of Maine, with a projected 70 percent cut for 2013. Meanwhile, the catch for yellowtail flounder on Georges Bank was slashed 80 percent last year and regulators project a 51 percent cut next year.

The huge cuts may be limited to certain species, but they threaten the entire industry. That’s because fish in New England waters mix, so the catch on even healthy species such as haddock must be tightly restricted to protect the struggling species they swim among.

The yellowtail cuts are even jeopardizing New England’s titanic scallop industry, which brought in $350 million in 2011. Because scallopers accidentally catch yellowtail, the fleet is subject to an annual catch limit. If it’s set so low that scallopers can’t help but hit it, that can lead to devastating restrictions.

The dismal condition of cod and yellowtail caught fishermen off guard. Just four years ago, cod in the Gulf of Maine, for instance, was considered robust. A recent assessment offered a new, bleak picture of its condition.

Bill Gerencer, a Maine-based seafood buyer and dealer, said the frequent “whipsaw assessments” of fish health are a sign that fishery regulation is being built on a deeply flawed scientific tool. “You can’t tell me you’re using the right tool if you can’t produce consistent, accurate results,” he said.

Goethel, the New Hampshire fisherman, said the current science excels at certain things but can offer only estimates on how many fish are out there. He said Congress has put a huge burden on the industry and regulators by wrongly requiring them to treat those estimates as far more solid than they are.

Fishermen emphasized that to build trust, scientists must involve them more closely in the assessment process and regularly interact with the fleet to know how it works. Regulators, meanwhile, stressed the need for fishermen to ensure they provide the accurate catch information they need to produce accurate science.

Bill Karp, the Northeast’s fisheries science chief, said it is critical for conversations between fishermen and scientists to continue. “There’s more to come,” he said.