ELLSWORTH -- Commercial fishing regulators have set a limit on the Atlantic herring catch that will greatly reduce the amount of the fish available to Maine fishermen for each of the next three years.

Meeting Tuesday in Newport, R.I., the New England Fishery Management Council voted to set the overall annual limit for herring at 106,000 metric tons.

The limit for this year was 194,000 metric tons, which means there will be 88,000 fewer metric tons available to purse seiners, canneries and lobster fishermen who rely on herring for their industries.

"It has huge implications for the state of Maine," Terry Stockwell, director of external affairs for the Maine Department of Marine Resources, said Tuesday evening. "Things are going to be very different."

According to industry officials, the lower limit was decided upon as a way to address scientific uncertainty in a benchmark stock assessment of herring that was conducted last year.

The fishery management council's science and statistical committee decided that earlier assessments did not account enough for unknown factors while estimating the health of the resource, officials have said.

According to DMR statistics, herring accounts for only 2 percent of the value of commercial fish landings in Maine and a little more than one-quarter of the overall volume.

But herring is used as the primary source of bait for Maine's lobster industry, which makes up more than two-thirds of all the value of commercial fish landed in Maine. In 2008, more than $235 million worth of lobster was caught in Maine.

Patrice McCarron, executive director of Maine Lobstermen's Association, said Tuesday that the new limit will have a significant impact on Maine's lobster industry, which already is struggling with lower lobster prices caused by a poor economy, expensive mandated gear changes and higher operating costs.

"It is very likely that we will experience bait shortages and even more likely that bait will be very expensive," McCarron said. "If bait prices double, a lot of fishermen won't make it (financially). I don't know what we're going to do."

The inner Gulf of Maine, known as Area 1A, is where most of the herring used as bait during the busy summer lobster season is caught. Regulators decided that only 26,500 metric tons of the 106,000 metric ton total limit will be available to the boats that fish for herring in Area 1A. This year, the annual limit for the inner gulf was 43,150 metric tons.

Officials said the limit for Area 1A could have been 10,000 metric tons, which would have been worse. But a reduction of approximately 17,000 metric tons still will be significant, they said.

Mary Beth Tooley of Camden represents Small Pelagic Group, a coalition of Massachusetts and Maine fishing boats. She said the lower limit conflicts with scientific surveys that indicate herring have not been and are not being overfished.

"The science really doesn't support such drastic measures," Tooley said Tuesday. "There's a lack of common sense in all of this. This means the next couple of years are going to be pretty trying."

Industry officials said they are trying to get NEFMC to conduct another benchmark assessment for herring as soon as possible, in the hope that it could convince the agency to raise the herring quota.

According to Stockwell, the next herring assessment is currently scheduled for 2012. If it is done sooner than expected, he said, the earliest it could be done is approximately one year from now, when next year's lobster season will be winding down.