BANGOR – Three Washington County salmon farming companies are violating the federal Clean Water Act by discharging pollutants, such as fish feed and waste, medications and non-native salmon, into the state’s water without the required permit, a federal magistrate said in a recommended decision issued this week.

U.S. Magistrate Margaret Kravchuk ruled that the companies were violating the federal law because they have not obtained pollution discharge permits from the U.S. Environmental Protection Agency.

However, the companies applied for the permits more than a decade ago and the federal agency, in concert with the Maine Department of Environmental Protection, has yet to develop standards for such licenses and, therefore, has not issued them.

In 2000, the EPA delegated authority to issue pollution discharge permits under the Clean Water Act in the vast majority of the state to the DEP. That agency has yet to complete pollution discharge permits for the aquaculture industry.

“This is every businessman’s nightmare: to be sued by an out-of-state environmental group because the federal regulators are not doing their job,” said Steve Page, the environmental compliance officer for Atlantic Salmon of Maine, the state’s largest aquaculture company.

The other two companies involved in the suit are Heritage Salmon, Inc. and Stolt Sea Farm.

Kravchuk’s ruling is only advisory and must be finalized by U.S. District Court Judge Gene Carter. He typically approves of her recommended rulings. The parties have 10 days to file objections to Kravchuk’s recommendation.

In three separate decisions issued Tuesday, Kravchuk ruled in favor of the two environmental groups and three citizens who initiated the lawsuit two years ago. The suit was filed by the U.S. Public Research Interest Group, the New England Law Center, Stephen Crawford of Eastport, Charles FitzGerald of Dover-Foxcroft and Nancy Oden of Jonesboro.

In addition, she recommended that a hearing be scheduled to determine, what, if any, civil penalty should be assessed against the companies, or if an injunction should be put in place to stop the companies from continuing to operate without a permit. However, she said, “the inaction and delay” of the EPA and state would be taken into consideration when determining a penalty or need for an injunction.

These groups were pleased with Kravchuk’s ruling.

“For over a decade, the Maine salmon farming industry has gambled that it could ignore the Clean Water Act with impunity. It has lost that bet,” said Bruce Merrill, a Portland attorney who represented the plaintiffs.

In her rulings, Kravchuk found that the companies were violating the act because they routinely discharge pollutants such as non-native fish, fish food that contains poultry parts and dies, and chemicals used to treat sea lice and other parasites into the water.

Further, Kravchuk said that EPA’s inaction on the permits did not excuse the companies’ action. Claims of “government inaction” cannot be used to discredit citizen suits like this one, Kravchuk wrote, otherwise the whole purpose of allowing such suits would be defeated.

Page of Atlantic Salmon said the companies were in a no-win situation, because they have inquired as to the status of their permits for years and “only heard silence.”

“It’s an unfortunate precedent that the companies are being sued for lack of action by the regulators,” he said.

In addition, he said, his company is not discharging pollutants into the water as Kravchuk said they are. ASM has not used antibiotics on its fish for two years because it vaccinates them in its hatcheries before they even reach the ocean. There is nothing in the fish feed that is not approved by the U.S. Food and Drug Administration. And, there is no evidence that the nonnative fish that are grown in the pens are interacting with wild Atlantic salmon, Page said.

The latter has been a major concern of the federal agencies that placed wild Atlantic salmon in eight Maine rivers on the endangered species list two years ago. The agencies cited the escape of farmed fish, and their potential to breed with and therefore dilute the gene pool of wild fish as a major reason for the listing. Since then, the industry has agreed to protocols to strengthen their sea cages in order to prevent the escape of farmed fish.

The ruling comes at a time when the industry is reeling from the forced killing of thousands of salmon. All farmed salmon in Washington County’s Cobscook Bay were ordered slaughtered earlier this year in an effort to stop the spread of infectious salmon anemia, a deadly disease that has decimated fish farms in Canada and Europe.

The bay is to remain free of fish for three months. When fish are put back into the bay, it will be at much lower densities than before.

A spokesman for the EPA said Wednesday that when the companies came to his agency to apply for the permits, the agency felt that other state and federal permits were adequate to deal with water quality concerns. Those permits were issued by the U.S. Army Corps of Engineers and the Maine Department of Marine Resources.

Since the EPA delegated permitting authority to the Maine DEP, it has been working closely with the state on the matter, said Mark Merchant.

Despite the lack of a permit, Page said he is “confident that we’re not harming the environment” because his company has been in compliance with the DMR monitoring program for more than a decade.