New England fishermen and scientists met Friday amid an industry crisis in a forum that aimed 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 they contradict with what they find at sea. And with key stocks struggling and huge projected cuts 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 New Hampshire fisherman David Goethel.

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

John Bullard, the head of the National Oceanic and Atmospheric Administration’s Northeast office, said fishermen and scientists shouldn’t be at odds since they 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 that live out of sight. They also took questions from fishing industry advocates frustrated over what they say are shifting and incorrect population estimates that have led to lower catch limits and damaged their businesses.

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 nearing for 2013. Meanwhile, the catch for yellowtail flounder in 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 together, 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 revenues in 2011. Since scallopers accidentally catch yellowtail, the fleet is subject to an annual yellowtail 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 and growing before a recent assessment offered a newly 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 that needs to be replaced.

‘‘You can’t tell me you’re using the right tool if you can’t produce consistent, accurate results,” he said.

Goethel said the current science excels at certain things but can offer just estimates on how many fish are out there. Still, 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 really 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 get them the accurate catch information they need to produce accurate science.

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

2012 Associated Press