EASTPORT – Sometime within the next three weeks, Washington County’s Cobscook Bay will be empty of farmed salmon for the first time in more than 13 years.

Bay fish farmers began removing the remaining 1.5 million salmon from their ocean pens Monday in response to a government plan to stop the spread of infectious salmon anemia.

The state Department of Marine Resources on Monday announced the order to slaughter the remaining Cobscook Bay salmon in coordination with the U.S. Department of Agriculture’s Animal Plant Health Inspection Service.

USDA is providing $8.3 million a year for the next two years to cover losses to Cobscook Bay fish farmers and to pay for disinfecting equipment and epidemiological programs to eradicate the disease.

Infectious salmon anemia kills salmon, but does not harm humans. The virus first was discovered in Norwegian fish farms in 1984 and decimated New Brunswick salmon farms in 1998.

It first was detected in Maine last February in Cobscook Bay. Since that time, there have been 17 outbreaks at 15 cage sites in the bay, according to DMR aquaculture coordinator Andrew Fisk.

Fisk said Cobscook Bay fish farmers destroyed more than 1 million salmon in the 10 months leading up to the DMR eradication order.

The order is necessary because all but one of the Cobscook Bay farm sites had detected ISA as of December, he said.

“There’s no magic bullet for this pathogen,” Fisk said. “We have to be cautious and we have to be thorough.”

The USDA will not reimburse the farmers for fish that were slaughtered before Dec. 13 when U.S. Secretary of Agriculture Ann Veneman approved the $16.6 million allocation.

Fisk said Heritage Salmon – a division of Connors Aquaculture Inc. – Stolt Sea Farm Inc., and Treats Island Fisheries, which is owned by Fjord USA, began removing fish from their pens Monday. Culling the fish will take approximately three weeks, and the effort is being supervised by USDA staff, assisted by staff from DMR and the Maine Marine Patrol.

The details of how much the salmon companies will be paid for their fish still are being worked out, Fisk said. Approximately $7 million of the $8.3 million a year in USDA funding will go to the salmon farmer for indemnification and to pay the cost of cleaning the sites and disinfecting equipment, he said.

Fisk said most of the Cobscook Bay fish have not grown to the market size of 6 to 12 pounds and cannot be sold. The USDA is approaching the Office of Management and Budget to get the full $12 million a year that was requested by Maine’s salmon industry, he said.

Once the fish are gone, the cages, barges and all equipment associated with the farms will be removed and thoroughly cleaned and disinfected, and the bay will remain empty of farmed salmon for 60 to 90 days, according to state Marine Resources Commissioner George LaPointe.

“By fallowing the bay for between 60 and 90 days, and disinfecting everything used on a farm, we will be making a significant reduction in the amount of virus that is present in the bay,” LaPointe said in a news release Monday. “We’re breaking the life cycle of the virus and any associated vectors, such as sea lice, and that’s going to give us a clean slate when we put the Bay back on line in the Spring.”

Fisk said the eradication of the Cobscook Bay fish is part one of a two-part program.

Salmon farmers will be permitted to reintroduce fish to the bay under a bay management plan, which is a new set of regulations that include a 25 percent reduction in the total number of fish in the bay and a two-year program in which only one half of the bay can be stocked in any given year.

The southern part of Cobscook Bay will be stocked this spring, and the northern half in 2003.

Historically there were more than 3 million farmed salmon in Cobscook Bay, Fisk said.

The reduction in stocking density will be determined on a farm-by-farm basis as part of each company’s permit to transfer salmon smolts from freshwater hatchery to grow-out pens in the ocean, he said.

The bay management plans also include stocking single-year class fish – assuring that all fish in a certain area are introduced to the water and subsequently harvested at the same time – continued use of biosecurity protocols, use of accredited veterinarians to monitor the health of the fish, submission of accurate and complete inventories and making mortality information available to the DMR.

Participation in the bay management program is mandatory for all salmon growers and includes salmon finfish farms in Maine.

The Cobscook Bay fish farms are the only salmon farms in Maine where infectious salmon anemia has been detected and Monday’s eradication order effectively includes all Maine farmed salmon that have been exposed to the disease.

The earlier slaughter of more than 1 million fish decreased the number of workers in Washington County’s salmon industry and the new eradication order is expected to result in more layoffs.

This fall, R.J. Peacock in Lubec laid off 60 of the 90 employees at its salmon processing plant. As of November, there were more layoffs – leaving nine workers at the plant, according to owner Robert Peacock.

Heritage Salmon employs approximately 135 full-time people when its Eastport salmon processing plant is in full production.

There was no answer at Heritage Salmon on Monday, but Eastport City Manager George “Bud” Finch said he believes the company laid off in excess of 35 people this fall.

Cobscook Bay is home to 28 of Maine’s 45 leases for finfish aquaculture and is the birthplace of Maine’s salmon farming industry.