For years, fishermen from Gloucester to New Bedford have accused the federal government of relying on faulty science to assess the health of the region’s cod population, a fundamental flaw that has greatly exaggerated its demise, they say, and led officials to wrongly ban nearly all fishing of the iconic species.

The fishermen’s concerns resonated with Governor Charlie Baker, so last year he commissioned his own survey of the waters off New England, where cod were once so abundant that fishermen would say they could walk across the Atlantic on their backs.

Now, in a milestone in the war over the true state of cod in the Gulf of Maine, Massachusetts scientists have reached the same dismal conclusion that their federal counterparts did: The region’s cod are at a historic low — about 80 percentless than the population from just a decade ago.

“The bottom line is that the outlook of Gulf of Maine cod is not good,’’ said Micah Dean, a scientist who oversaw the survey for the Massachusetts Division of Marine Fisheries. “What we’ve seen is a warning sign about the future of the fishery, and it’s a stark change from what we saw a decade ago.’’

The state’s surveys, conducted on an industry trawler, also found a dearth of juvenile cod and large cod, suggesting that the population could remain in distress for years. The lack of small cod reflects limited reproduction, while the absence of the larger fish is a problem because they’re capable of prolific spawning.

Dean said he hoped fishermen would find the results credible, given that the survey sought to accommodate their concerns about the federal survey, conducted by the National Oceanic and Atmospheric Administration.

To address their concerns, the state spent more than $500,000 to trawl for cod in 10 times as many locations. Rather than sampling the waters twice a year, as NOAA does, the state cast its nets every month from last April to January, and kept them in the water about 50 percent longer. They also searched for the fish in deeper waters, where fishermen have said they tend to congregate.

“It was an exhaustive survey meant to provide an answer to the questions that the fishermen were posing,’’ Dean said. “But the fish weren’t there.’’

Some longtime cod fishermen remain unconvinced. They say the historic fishery has been fully rebuilt, although the federal and state surveys estimate it is only about 6 percent of the level needed to sustain a healthy population.

Vito Giacalone, policy director of the Northeast Seafood Coalition in Gloucester, which represents many of the region’s commercial fishermen, maintained that the state surveys had some of the same flaws as the federal surveys. Rather than conducting random sampling throughout the Gulf of Maine, the researchers should have trawled for cod in areas where fishermen are finding them, he and other critics said.

“The state survey literally does zero to improve our confidence,’’ said Giacalone, who served on a committee that advised state scientists on conducting the survey. “You can’t just sample anywhere. You have to go to where the cod are supposed to be.’’

Giacalone and others from the industry said the surveys have failed to capture what fishermen are seeing on the water.

“Where these fish exist in the western Gulf of Maine is greater than it has ever been in my lifetime,’’ he said.

Dean and other scientists said random sampling is a vital tool for any objective measurement of the cod population. Sampling only certain areas could skew the results.

Scientists say there is an explanation for what fishermen are seeing, particularly those from Gloucester. Cod tend to cluster when their numbers decline, and the fishermen know where to find them. Many of the remaining cod are in waters near Gloucester.

They also say that many Massachusetts fishermen are not seeing the areas where there are no cod left, such as the eastern Gulf of Maine, or how few juvenile cod remain, as their nets are designed to allow smaller fish to escape.

“The state’s findings give us confidence in our assessment results and that we’re not getting a false sense of the population size,’’ said Mike Palmer, a biologist who oversees the region’s cod assessment for NOAA.

John Bullard, NOAA’s regional administrator who in 2014 cut cod quotas by about 95 percent, said he takes no joy in the state survey results.

“I would like nothing more than that survey to have found lots of cod, because there’s nothing I’d rather see than the cod population rebuilding,’’ he said. “But it doesn’t look like the Massachusetts survey is showing that, and that’s heartbreaking.’’

The state paid for its survey mainly with federal emergency funds designated by Congress to aid the fishing industry. State environmental officials declined to say how much longer the surveys will be conducted, but they are scheduled to resume this month.

The administration “looks forward to another year of collecting critical information that improves the assessment,’’ Katie Gronendyke, a spokeswoman for the state Executive Office of Energy and Environmental Affairs, said in a statement.

Future surveys could incorporate non-random sampling and new methods using video cameras, as the fishing industry has urged, she said.

Steve Cadrin, a professor of fisheries at the University of Massachusetts t Dartmouth, said the state surveys have gone a long way to addressing the industry’s concerns, but still miss far too much of the Gulf of Maine. “Until we have survey techniques that can sample a much larger portion ... we’re not going to have very precise estimates,’’ he said.

For fishermen like Joseph Orlando, who has spent more than 40 years catching cod out of Gloucester, the limits on the surveys and the amount of cod he still catches cast doubt on the state and federal findings.

“There’s definitely something wrong with the science,’’ he said. “We’re out on the water constantly — all year round — and what we see and what they see is completely the opposite. I don’t know what to say anymore.’’

David Abel can be reached at dabel@globe.com. Follow him on Twitter @davabel.