PORTLAND – A federal judge Friday found Maine’s largest aquaculture company in civil contempt for violating his order that barred it from stocking a new class of young salmon in its pens.

U.S. District Judge Gene Carter concluded that Atlantic Salmon of Maine sought to evade his restriction by purchasing and stocking smolt through its wholly owned subsidiary, Island Aquaculture Co.

Carter ordered Atlantic Salmon to halt any further sales of smolt to Island Aquaculture for introduction into pens in Maine and to pay a $100,000 penalty for each day that any future violations occur.

In addition, Atlantic Salmon must remove all smolt that Island Aquaculture stocked on or after April 30.

The judge set a May 28 deadline for the complete removal of smolt from the pens and ordered Atlantic Salmon to pay $10,000 for each day thereafter that any of the pens are not fully fallow.

Carter’s Feb. 13 order barred Atlantic Salmon from stocking any of its pens at its seven farms until a water quality lawsuit filed two years ago by the United States Public Interest Research Group is resolved.

The suit accuses Atlantic Salmon and another Washington County salmon farming company, Stolt Sea Farm, with violating the Clean Water Act by not possessing permits to discharge pollution into the ocean. Those pollutants, including excess feed, feces and medications, are harming the environment, the suit alleged.

Carter ruled against the fish farms and held a hearing last October to set penalties. No decision on penalties or remedial action has been announced and it’s unclear when the lawsuit will be resolved.

Unlike Atlantic Salmon, Stolt did not plan to stock fish before spring 2004 and thus was not named in Carter’s February order. But Atlantic Salmon advised the court that it intended to stock its pens, probably during the first two weeks in May.

The court then issued its prohibition on stocking fish as a way to preserve the status quo and block Atlantic Salmon from evading the potential impact of penalties still under consideration.

Friday’s 30-page ruling concluded that Atlantic Salmon had complete control over the affairs of Island Aquaculture, which the judge characterized as “simply a conduit through which ASM flows fish, feed and services necessary to raise and harvest merchantable farm-raised salmon.”

The court found that Atlantic Salmon used Island Aquaculture to sidestep the Feb. 13 order to avoid the prospect of a $1.9 million to $2.5 million loss if it could not put the fish in its pens.

The decision by Atlantic Salmon to “sell” the smolt to Island Aquaculture was a sham because the subsidiary’s pens were in reality those of the parent and no money actually changed hands, the opinion stated.

Carter pinned responsibility on Atlantic Salmon and found nothing to indicate that Island Aquaculture’s manager participated in or was even consulted about what was being done.

Atlantic Salmon owns and operates five salmon farms in Machias Bay and two salmon farms in Pleasant Bay.