AUGUSTA – Sixteen organizations were approved Thursday as participants in the state’s effort to draft a general permitting system that would allow Maine fish farms to operate legally.

Maine’s 44 aquaculture operations, which stretch from Eastport to Blue Hill, are all technically in violation of the federal Clean Water Act because they have not been granted permits certifying that their pens do not cause environmental damage. For 20 years, Maine’s environmental regulators have assured new businesses that such permits were not necessary, and regulated aquaculture solely through a site approval process and fish transfer permits.

In response to a successful lawsuit filed against two Washington County aquaculture operations, however, the federal government last year directed Maine’s Department of Environmental Protection to design and grant water quality permits.

The general permit currently under discussion would encompass all but one existing fish farm. That and future businesses that do not fit under the umbrella of the general permit due to their environmentally sensitive locations must apply for individualized permits.

In September, the Board of Environmental Protection, the citizen group that interprets and enforces environmental laws, took jurisdiction for the general permit effort at state regulators’ request after months of unsuccessful negotiations.

Almost all criteria listed in a draft general permit is controversial. Environmentalists fear that excess feed from the aquaculture pens could result in algae blooms; they doubt the ability of tidal action to remove waste from beneath the pens; and they question the impact of large-scale aquaculture on the bay as a whole.

Perhaps the most contentious issue is the question of whether non-native or genetically altered salmon will be permitted in Maine pens. Some fish farms claim these salmon are hardier than native strains, but some biologists fear that the fish could escape and wreak havoc on efforts to preserve the federally endangered Atlantic salmon native to nearby rivers.

In fact, the EPA has already told Maine that any permit that allows genetically modified fish will not be accepted.

Eighteen groups applied to be included in the aquaculture permit hearing Thursday, and 16 were judged to have a “direct and substantial interest” in the matter.

Successful participants include; Heritage Salmon; the Maine Aquaculture Association; Maine Salmon Inc.; a coalition of six businesses including the two cited in the pending lawsuit, Atlantic Salmon of Maine and Stolt Sea Farms; the U.S. Public Interest Research Group; the Atlantic Salmon Federation; the Maine Sierra Club; Trout Unlimited; the Conservation Law Foundation; the Roque Island Gardner Homestead; the city of Eastport; the town of Lubec; the Sunrise County Economic Council; the Zone C Lobster Council; Friends of Blue Hill Bay and the East Penobscot Bay Alliance.

Such a high number of participants is unprecedented, said a BEP staff member Tuesday.

In the board’s formal hearing process, each of the participants has the right to present expert witnesses and to cross-examine the witnesses brought by other participants.

With 16 participants, the hearing could quickly become chaotic, said board Chairman John Tewhey of Gorham. He reserved the right to consolidate the 16 participants into broad interest groups to speed resolution.

Later this month, all participants will meet to set a schedule for the hearing, which likely will begin in January.