BOSTON — New England fishing regulators on Wednesday moved to determine whether herring trawlers, with their massive nets and brutal efficiency, are wiping out sea herring and doing lasting damaging to other struggling northeastern species.

The herring industry says the often repeated charge is baseless, and there’s no reliable evidence their boats are threatening either the industry or the ecosystem.

On Wednesday, regional fishing managers voted to require independent monitors on every trip of the largest herring vessels that work waters off New England. Both the industry and its critics backed the requirement Wednesday, confident they’ll be vindicated when the observers report what the trawlers do and don’t pull up.

“We need to clear the air of all the lies that’s been spoken over the last five years,” said herring fisherman Peter Mullin during the council meeting in Portland, Maine.

The measure approved by the New England Fishery Management Council isn’t expected to go into effect until at least spring 2013, as the industry and managers figure out how pay for it.

The tiny herring — no more than a foot long — are eaten pickled, but they’re far more often sold as bait for more valuable species, such as lobster. They’re seen as crucial by environmentalists and fishermen as prey for numerous important species, from striped bass, to sea birds, to whales.

Herring, a schooling fish, gather in masses that sometimes extend miles. The largest herring boats, called mid-water trawlers for the part of the water column they work, tow 100-yard long nets between them and can pull up hundreds of thousands of pounds of herring at a time. The new measure targets them, not boats that pull up the fish unintentionally.

Critics say the large trawlers aren’t just depleting herring stocks, they’re inadvertently sweeping up struggling species such as cod along the way, preventing their populations from rebounding.

They also say trawlers are snaring the river herring that sometimes mix with sea herring, hurting the local ecology and thinning out traditional “herring runs” that occur each spring, when residents watch the fish return to upstream birthplaces to spawn.

Anecdotal stories abound about rich fishing areas going all but dead once the trawlers pass through.

“I’ve heard these claims of a clean fishery, not much dumping,” Darren Saletta of the Massachusetts Commercial Striped Bass Association, told the council. “Then you see these boats come through with nets the size of football fields and just clean the place out.”

But the trawlers say herring are abundant, and that the observations to date show that they aren’t pulling up large amount of unwanted fish.

They say people look at the hulking boats, which can be as long as 165 feet, and make bad assumptions about the damage they do and the people who run them.

Jeff Kaelin, of Lund’s Fisheries on Cape May, N.J., which fishes for herring, said he was looking forward to seeing the observers absolve the industry.

“I’m pleased today that this long process of innuendo and accusation and class warfare … may actually be coming to an end,” he said.

After the vote, the cost of the observers emerged as a major issue. Earlier this month, the National Marine Fisheries Service told the council it didn’t have money to fund additional herring observers. The industry says it’s willing to pay $325 for each observer, each trip, but that’s well below a projected cost of $750 per day.

Council members eventually voted to delay their measure for a year, until the industry and regulators figure out how to pay for the monitors. The status quo includes monitors on some, not all, of herring trawler trips.

“I don’t see any other way forward here,” said council member David Goethel, a New Hampshire fisherman. “People may not like it, They may think that it’s dragging your feet, or whatever. But these are not simple legal questions.”