The controversy over whether the state should have the authority to issue federal water pollution permits – a debate that has gotten the governors of two Indian tribes declared in contempt of court – became much more complicated Monday when wild Atlantic salmon in several Maine rivers were declared an endangered species.

Now, the U.S. Environmental Protection Agency – which is already months behind in making a decision – must consult with two federal fisheries agencies to determine whether giving the state Department of Environmental Protection the authority to issue permits under the Clean Water Act will harm the fish.

“It presents an additional hurdle we have to cross,” Tim Williamson, an EPA attorney, said Tuesday of the salmon listing. Knowing that the salmon decision was coming, he said, EPA officials had already been discussing the situation with fisheries officials, but he added that now those talks would have to be more formal.

On Monday, the U.S. Fish and Wildlife Service and the National Marine Fisheries Service announced that wild Atlantic salmon in eight Maine rivers had been placed on the federal endangered species list.

The listing, which federal officials said was necessary because the fish are on the brink of extinction, further complicates the state’s case that it should have the authority to issue federal water regulation permits. Forty-four states have already been given the power, but they didn’t have Atlantic salmon or Indian tribes contesting the delegation of authority to deal with.

In announcing the listing, federal officials made it clear that they did not think the state was doing an adequate job protecting the salmon.

“The Maine plan was excellent – as far as it went. But, it left some big ticket items out,” said Paul Nickerson, endangered species specialist for the U.S. Fish and Wildlife Service’s Northeast Region.

The items left out included a plan for blueberry growers to withdraw irrigation water from the rivers, eliminating the use of European strains of salmon by fish farmers and the use of stronger cages to prevent the escape of farmed fish.

The conclusion that the state’s salmon conservation plan is not adequate could lead other federal agencies to wonder if the state is capable of doing an adequate job of regulating water quality, the EPA’s Williamson acknowledged.

In contesting the application for permitting authority, the Penobscot and Passamaquoddy Indian tribes have said they do not believe the state is up to the job because it is beholden to paper companies, all of which have permits to dump treated wastewater into rivers and streams.

The interplay of the salmon listing and discharge licenses furthers the uncertainty harming the state’s business climate, said Jeff Toorish, executive director of the Maine Pulp & Paper Foundation. “It does show that the absolutely misguided listing of salmon is going to have broad implications far beyond what has been considered,” he said.

“Maine jobs are going to disappear. I’m convinced of that,” Toorish added.

To streamline the permitting process, the state last fall applied to the EPA for authority to issue federal discharge permits. The Penobscot and Passamaquoddy tribes contested the application because they believe the federal government will do a better job of protecting their interests.

The EPA was supposed to act on the state’s application within 90 days, but the agency twice, with the state’s acquiescence, extended the deadline.

At the end of September, the DEP called for a quick decision. Since then, the EPA’s authority to issue the discharge permits has been suspended, as required by law. But, the state hasn’t been given permitting authority, so currently no entity can issue the federal permits that are required to discharge wastewater under the Clean Water Act.

“It leaves … the whole state in limbo,” said Matt Manahan, an attorney for 30 paper companies and municipalities that support the state’s application for permitting authority.

Under the current situation, a company that planned to open a new facility in Maine or expand an existing facility that needed a federal permit would not be able to get one. Industry officials were not aware of any company that was in that situation.

However, Manahan said: “It’s definitely a problem and we’re concerned about it.”

Again, this situation appears unique to Maine.

“To my knowledge these lapses don’t happen often,” the EPA’s Williamson said. “But, I can’t say that it’s unprecedented.”

Also on Monday, three tribal governors representing the Penobscots and Passamaquoddies avoided jail by appealing to the Maine Supreme Judicial Court a superior court judge’s decision finding them in contempt for not turning over to paper companies documents related to water quality regulation.

As part of the ongoing debate over whether the state or federal government should issue federal discharge permits, three paper companies had requested the tribal documents under the Maine Freedom of Access law.

Lawyers for the Penobscot and Passamaquoddy tribes contended that the tribes, as sovereign entities, were not subject to access law, and that the documents, including minutes of tribal council meetings, were private and could not be turned over.

Superior Court Judge Robert Crowley disagreed, ordering the three men jailed unless the documents were turned over or his decision appealed.