The Canadian Food Inspection Agency recently allowed Cooke Aquaculture to continue to raise open-pen salmon after they contracted infectious salmon anemia (ISA).
The Atlantic Salmon Federation says due to the contagious nature of the disease, the decision poses a risk to wild salmon in the region.
Bill Taylor, the federation's president, said in the absence of strict guidelines to eradicate ISA in Atlantic waters, the next best option is to move farmed fish to land-based tanks.
"It is cost competitive and you absolutely eliminate any chance of this sort of disease outbreak," said Taylor.
"It's fully contained, the fish can't escape — it's best of both worlds."
According to the CFIA, the disease kills up to 90 per cent of infected fish. Symptoms include a loss of appetite, abnormal swimming patterns, grey gills, or a swollen abdomen.
The virus can spread in contaminated water or by contaminated equipment.
However the CFIA stresses that ISA is not a risk to human health and that salmon with the virus are safe to consume.
Last summer, the disease was discovered at an aquaculture site in Shelburne, N.S.
Two cages at the Nova Scotia facility, which contained smaller salmon, were immediately destroyed.
However, 240,000 fish that were close to market size were allowed to continue growing. Those fish were then transported to Cooke Aquaculture's plant in Blacks Harbour, N.B., to be processed for sale.
The decision to allow fish, which are positive for ISA, to remain for half a year in their cages and then to be transferred to a different province for processing, points to a change in CFIA policy.
"The accepted mode of operation right up until this incident has been to — once you identify the site has ISA — is to get those fish out of the water as quickly as possible and disposed of," said Taylor.
"In this case the fish were left in the water for many months, grown to maturity and now — I understand it — they're going to market. So, personally, I don't like the idea of eating diseased fish or diseased chickens or diseased meat of any kind."
Taylor said he's still waiting for an explanation on why the CFIA made the decision it did and whether Fisheries and Oceans Canada knew about the agency's change of direction to control the virus' spread.