AUGUSTA – The majority of Maine’s salmon farms now have a means of doing business legally under the federal Clean Water Act.

The state Board of Environmental Protection on Thursday approved a long-awaited general finfish aquaculture permit that provides strict guidelines for protecting water quality in the Atlantic Ocean.

The board rejected a last-minute compromise agreement supported by the aquaculture industry and brokered by the governor’s office.

The farm sites that meet all of the criteria could have their five-year permits in hand by early July, said Dennis Merrill, the Department of Environmental Protection staff member in charge of the permit process.

The state has been wrestling with this issue for more than 10 years, most recently in response to a lawsuit filed by environmental groups against Maine’s largest salmon farms.

U.S. District Judge Gene Carter ruled that operating without a discharge permit from the U.S. Environmental Protection Agency violated the Clean Water Act, and he chastised state and federal officials for not moving quickly enough on the issue.

The BEP, a citizen group appointed by the governor to advise the DEP commissioner on policy and enforcement issues, took sole responsibility for the aquaculture permit issue last year with the blessing of the EPA.

The one-size-fits-all permit was designed to make the application process simpler for fish farms. But drafting the permit under the board’s formal procedures has been anything but easy. Sixteen intervening parties, including towns, aquaculture companies, environmental groups and representatives of other fisheries, participated in the lengthy process.

Since two companies, Stolt Sea Farm Inc. and Atlantic Salmon of Maine, are subject to orders from a federal judge to acquire permits as soon as possible, the board was determined to get the permit approved Thursday. In its rush, it rejected some small changes for fear it might drag out the process.

“[The permit] should not be tinkered with and nibbled to death,” said Jeff Baylor, a spokesman for Atlantic Salmon of Maine.

Geographically, the final permit covers most of Maine’s existing salmon aquaculture operations. However, waters south and west of Naskeag Point in Brooklin, all the way to Kittery, are not covered by the permit because fish aquaculture doesn’t exist in those communities. Most of Frenchman and Blue Hill bays are excluded because the currents there are less powerful, and thus less able to flush waste out of a fish farm.

An attempt to have the waters around Roque Island, just east of Jonesport, excluded from the permit because of the pristine nature of its water was unsuccessful, despite support from three board members, including Ernest Hilton. He cast the sole vote against the aquaculture permit because of his concern about the island.

Successful applicants falling within the geographic boundaries also will have to meet basic criteria such as current velocity, fish density limits and proper distance between the sea floor and the bottom of pen nets.

DEP officials make the final ruling over whether an application meets the criteria. Applicants for sites that do not must apply for an individual permit, which involves a longer process.

The permit also lays out a strict schedule for removing non-North American salmon from Maine waters in an effort to protect the state’s tiny population of federally endangered Atlantic salmon – a major priority for the EPA. Companies must stop stocking nonnative fish by July 31, 2004, and must remove all fish that are found to be anything but genetically native, by Sept. 15, 2006.

However, the permit also includes a controversial “alternate compliance plan” that would extend the final deadline to Dec. 31, 2008, provided the companies promise to take action “as soon as possible.” Merrill said that the plan was necessary because the availability of native salmon eggs and smolt is unknown.

The permit requires that all farmed salmon be marked in order to be identifiable by farm by July 2007.

The permit requires state notification of all medication use. In a close vote, the board decided to allow prophylactic use of antibiotics – a worry to some environmentalists – without prior approval by the state.

“No one wanted to get in the way of a veterinarian’s practice of medicine,” Merrill said.

Several salmon sites will be unable to meet all of the general permit criteria without major changes to their operations.

A compromise brokered by the governor’s office and rejected Thursday by the BEP would have allowed all existing farm sites to get temporary permits, whether they meet criteria or not.

The deal would have been beneficial for ASM and Stolt, which will appear in the First Circuit Court of Appeals July 29 to fight Judge Carter’s ruling. Having permits in hand would improve their position.

However, the board unanimously rejected the deal, which several members saw as an attempt to usurp their authority. A representative from the Attorney General’s Office said that the compromise would render the permit criteria “meaningless.”

DEP Commissioner Dawn Gallagher apologized to the board for its exclusion from the meetings that led to the compromise deal. The governor’s staff held a private meeting with ASM at the company’s request, which was followed by a meeting at the governor’s office to which all 16 intervenors were invited.

Board members breathed a sigh of relief at the permit’s approval Thursday, but they realized the debate is not over. Lawsuits challenging specific criteria are likely.

“I’ve watched this process since 1989, and I didn’t think it was ever going to come to an end,” said board member John Marsh. “This is going to be in court as long as I’m alive, probably afterward, but we’ve got [to] do something.”