Cooke Aquaculture says about 240,000 fish will be transported from its farm off Coffin Island near Liverpool, N.S., to a fish plant in Blacks Harbour, N.B., over the next month. The processing started last week, it said.
Cooke is the first company to process salmon with the disease under new protocols set out by the Canadian Food Inspection Agency, company spokeswoman Nell Halse said.
The federal agency said the virus does not pose a risk to human health and is safe for consumption.
"They're perfectly safe to eat," said Halse."In this case we've got fish that are market size. There's nothing wrong with them from a human health perspective.
"It's really only an issue for fish health. It's nothing to do with human health."
Halse said Canadian Food Inspection Agency officials have been at both sites over the past six months developing proper guidelines for the processing.
That includes disinfecting the fish plant and setting protocols for managing the waste water in the tanker trucks that transport the fish.
Halse said everyone involved has gone through strict training on how to handle the fish to prevent the virus from spreading.
"All of the boat captains, the truck drivers, the plant workers have all been trained to know how to handle these fish so that there's no possibility of the virus getting back out into the ocean or going to other farms."
Last spring, Cooke had to kill hundreds of thousands of salmon because of an outbreak of infectious salmon anemia in pens outside Nova Scotia's Shelburne Harbour.
Halse said those fish were killed because they were only halfway through production and too small to be marketed.
She said a different strain of the virus was detected at its Coffin Island farm last June, so the site was quarantined and the salmon were grown to full market size.
If the federal agency doesn't order the fish to be killed off, the farmer is obligated to process and market the fish, said Halse. The government compensates salmon growers in instances that a cull is ordered.