The Canadian Food Inspection Agency confirmed Wednesday that infectious salmon anemia has been found at a facility in the province. The agency declined to name the operation, citing privacy concerns.
However, a spokeswoman for Cooke Aquaculture said the virus was discovered at the company's operation in Shelburne Harbour.
"We don't take this lightly," Nell Halse said from the company's headquarters in Saint John, N.B.
"No farmer wants to lose any of their animals to a virus or to a disease. This is never good news for a farmer."
The federal inspection agency said the virus does not affect human health or food safety. It can, however, kill up to 90 per cent of infected fish depending on the strain.
Joanne Constantine, national manager for the agency's aquatic animal health division, said measures are being taken to prevent further spread of the disease. Pens, cages and equipment will be disinfected and testing will continue on the rest of the salmon at the facility.
"We'll monitor the farm's mortality rate, sampling fish, looking for signs of disease to inform us as to what's happening with the farm going forward," Constantine said from Ottawa.
The agency began taking samples after Cooke Aquaculture reported a possible outbreak last month. The company said it destroyed two cages of fish after routine testing raised concerns.
Constantine said the agency will order that a third cage be destroyed with compensation paid to the company. If more cases of salmon anemia are discovered, the agency said more fish could be destroyed.
Halse said she did not know when the third cage would be destroyed.
"In an ideal world, that proactive measure will protect the rest of the farm, but we also know that we can't assume that," she said.
"There's heightened biosecurity on the farm and our hope is that we will be able to grow the rest of the fish out as healthy fish until they reach market size."
The company remains under quarantine. Constantine said there is no timeline on when the quarantine will end.
"When the fish are eventually harvested and the site is cleaned and disinfected, (if) the CFIA is satisfied that the risk of disease no longer exists, then the quarantine will be lifted," she said.
There are 13 salmon farming operations in Nova Scotia. Cooke Aquaculture operates nine of them, including two in Digby County, and four in the Shelburne Harbour and McNutts Island areas.
Halse could not say what the loss of the salmon would have on the company's bottom line. She said discussions surrounding compensation were ongoing with the Canadian Food Inspection Agency.
She said the company has dealt with salmon anemia in New Brunswick in the past.
Opponents of the aquaculture industry have expressed concerns that the presence of salmon anemia could link wild salmon decline with fish farms.
The source of the disease remains unknown. Critics of salmon farms blame the industry, but the industry vigorously contests the allegations.
The Canadian Food Inspection Agency said the disease is known to exist in the waters off Nova Scotia, Prince Edward Island and New Brunswick.