For the first time in more than three months, farmed salmon are swimming in ocean pens in Cobscook Bay.

“We’re restocking, and we’re excited about it,” David Morang, manager of Eastport operations for Heritage Salmon, said Friday.

The 1.2 million salmon that are being put into Cobscook Bay within the next few weeks will be ready for harvest in approximately 18 months.

This week’s permission from the Maine Department of Marine Resources to restock the lower half of Cobscook Bay is the first positive news for area fish farmers since infectious salmon anemia, or ISA, was detected in a salmon aquaculture site off Treat Island in February 2001.

More than 160 people have been laid off in the last year, and the four large aquaculture companies that operate in Cobscook Bay have slaughtered or harvested early more than 2.3 million farmed salmon in the waters off Eastport and Lubec.

Most of the job loss occurred in the processing end of the industry, including 125 salmon processors in Lubec and Machiasport, who lost their jobs early on in the 10 months after the first outbreak. A total of about 900,000 fish died of the virus or were harvested below normal market size during that time as farmers attempted to salvage what they could.

Those 900,000 fish were worth almost $11 million, according to the Maine Aquaculture Association.

As the disease continued to spread, MAA, the Maine Department of Marine Resources and the Maine State Veterinarian approached the U.S. Department of Agriculture Animal and Plant Health Inspection Service for help in controlling the virus and reimbursing farmers for their losses.

In December, federal Secretary of Agriculture Ann Veneman declared the ISA in Maine-farmed salmon an emergency and authorized $8.29 million in USDA assistance.

Of that total, $7.2 million was to be used to reimburse salmon farmers for slaughtering the remaining 1.5 million salmon in Cobscook Bay and cover the cost of cleanup operations.

Acting on that approval, DMR issued a Jan. 7 order for farmers to depopulate the bay.

By the end of January, all remaining farmed salmon in the bay had been slaughtered.

Also in January, another 32 workers were laid off from an Eastport processing plant, according to the Maine Department of Labor. The plant is owned by Heritage Salmon, and calls made Friday to a company spokesman asking when those people would go back to work were not returned.

Maine’s salmon aquaculture industry employs approximately 540 people, according to DMR aquaculture coordinator Andrew Fisk.

Just over 370 of those workers are in Washington County, and the 160 layoffs include 76 people who were laid off from Nordic Delight in Lubec, which processed for the industry. The Nordic employees are not included in the 540 people directly employed in the salmon aquaculture industry. Nordic Delight just received news that its workers would receive extended unemployment compensation.

Stolt Sea Farm Inc. has closed its Lubec processing plant – putting 11 people out of work. The company does not plan to reopen.

David Peterson, chief executive officer of Atlantic Salmon of Maine, said last month that 40 people from the company’s Machiasport plant were laid off because of ISA, but he expected at that time to back in full production by the end of May.

The three-month cleanup of Cobscook Bay – including hand-scraping and steam-cleaning salmon pens and other equipment – kept many people working, but the industry is now facing additional problems.

Just as the cleanup of the bay was nearing completion and companies were preparing to restock, USDA announced the proposed reimbursement schedule for the salmon killed as a result of the Jan. 7 depopulation order.

USDA is proposing to reimburse the farmers for 60 percent of production costs for the lost fish, all of which were too small for the market.

Fish farmers, who were expecting a 100 percent reimbursement, have until June 10 to respond to that proposal.