Atlantic salmon farming is one of the most polarized and politicized industries in the state. But this week, the aquaculture companies, regulators and environmentalists who are struggling to come to terms with a federal judge’s scathing judgement of the industry agree on one thing: Sweeping change is inevitable.

“These are full-body blows it will be very hard to recover from,” George LaPointe, Maine’s commissioner of marine resources, said Friday. “It will change the operations of everybody involved.”

Among the blows:

. Salmon farming, a $100 million business that employs about 1,000 Mainers, will nearly shut down, on a rolling basis, for two years to allow the sea floor to recover from the negative environmental impacts of food and feces raining down from salmon pens.

. European-descent salmon, which make up the vast majority of the farmed fish in Maine, are now banned, for fear that they will escape their pens and spread their genes or diseases to the handful of endangered wild Atlantic salmon that still live in some Maine rivers. Thousands of fish may have to be destroyed.

. State regulators and salmon farmers will each have to rewrite their policies to take more responsibility for ensuring, with new tests and procedures, that salmon farms do not pollute the Atlantic Ocean.

Wednesday, U.S. District Court Judge Gene Carter issued his ruling in the penalty portion of a civil suit brought by environmental groups against two of Maine’s largest aquaculture companies, Atlantic Salmon of Maine and Stolt Sea Farms. Carter wrote a critical decision lambasting both the industry and the state and federal employees charged with regulating it.

The lawsuit, filed last year by the U.S. Public Interest Research Group and the New England Environmental Law Center, accused Maine’s largest salmon companies of violating the Clean Water Act by polluting the ocean with medicines, fish food and feces without a discharge permit issued by the Department of Environmental Protection. Last June, Judge Carter agreed.

This week, he fined each company $50,000 and said that they may only continue farming if they meet his long list of requirements, many of which completely rewrite state policies on aquaculture.

The judge criticized state and federal regulators’ “foolishly naive expectation … of self-regulation.” For 13 years, no one required salmon farms to apply for federal pollution discharge permits, because each believed it to be the responsibility of some other agency.

“Entities causing the environmental harm have been given a free pass to continue their heedless despoiling of the environment,” Carter wrote.

But however hard he was on regulators, the judge also accused the companies of exploiting their 13 years of limbo. The companies did apply for the pollution discharge permits for each of their aquaculture sites, but didn’t follow up when it became clear that the permits hadn’t been issued, according to the judge’s ruling.

Now, as a result of his ruling, no fish may be stocked in the companies’ pens, most of which are located in Cobscook Bay off Washington County, until the state completes its work on a general aquaculture pollution discharge permit that will apply to most sites. The Board of Environmental Protection has been struggling with the details of the permit for over a year, and is expected to vote on a draft during its June 19 meeting.

Salmon farms aren’t worrying about the dates, however, because Carter’s ruling also states that pens currently in use must lie fallow for two years. Neither company has enough permitted lease sites to implement that kind of rotation. Currently, the typical rotation schedule is between 30 and 90 days.

“OK, you’ve got your permits, but where are you going to put your fish?” asked Sebastian Belle of the Maine Aquaculture Association.

Problems for Atlantic and Stolt, both of which are subsidiaries of Norwegian aquaculture companies, mean problems for the whole industry, he said. The two defendants make up nearly half the farmed salmon production in the state. Atlantic Salmon of Maine has between 1 and 2 million fish in the water at any given time, and produces 10 million pounds of fish each year. Stolt Sea Farms had a half-million fish in its pens during most of the year, and produces about 2 million pounds of fish annually.

“Independent farmers are a very, very small part of the industry,” said David Nicholas, an attorney for the National Environmental Law Center in Boston. “And we know that when the big guy makes changes, everyone else has to follow.”

But those changes will be painful, spokespeople for both companies said Friday.

Atlantic Salmon of Maine, which is based in Belfast, had been planning to stock fish this May and June, and recently was fined by Judge Carter because one of its subsidiaries put fish in the water. Stolt Sea Farms, which is based in Lubec, is scheduled to stock its pens this fall.

Now, they may have to wait until 2005.

“We can’t do business that way,” said Steve Page, compliance officer for Atlantic Salmon of Maine.

His company may have to destroy thousands of salmon fry in its hatcheries, even though scientists have not yet developed a test to tell which fish are European.

“You can’t tell by looking at them,” Page said. “That’s the catch-22 we’re in. We’re told we have to remove these fish, but we don’t know which fish they are.”

Stolt Sea Farms has been breeding out European genes, and believes that many of its fish would be considered North American. But the scientific uncertainty about genetics has company Vice President Shirley Roach-Albert concerned.

If both companies were to shut down or withdraw from Maine completely, the loss to Maine’s economy would be upwards of $350 million, Belle said.

Even if the companies strike a compromise soon and are somehow able to move forward with their scheduled fall stocking, the financial loss will be damaging. Neither company has shown a profit since 2000, both are dealing with the effects of a harsh winter, and Atlantic Salmon of Maine lost many of its fish when its Ebden hatchery caught fire earlier this month.

“There’s no question … [losses are] in the multimillions already,” Belle said.

The very image of Maine as a good place for aquaculture is at risk, he said, citing his organization’s estimate that the state lost between $10 million and $15 million in aquaculture investments while the legal battle was raging.

Nicholas has little pity for companies that he says had ample opportunity to change with the times. Responsible companies won’t be at risk of losing jobs, he said.

“If they’d spent half the energy and resources that they did in fighting the lawsuit and put that into improving the environmental situation, we would all have been where we needed to be much earlier,” he said.