The Canadian Food Inspection Agency ordered Cooke Aquaculture to kill and dispose all of its salmon at a fish farm in Shelburne Harbour, the same site where infectious salmon anemia was detected in February during routine testing.
At that time, the federal agency directed the company to kill fish in two pens and quarantine its site, but it said Thursday that more cases of the disease have since been confirmed.
Nova Scotia Fisheries Minister Sterling Belliveau said he is confident the virus hasn't spread beyond Shelburne Harbour.
"This is one area that has been quarantined and has been heavily monitored," Belliveau said, adding that he didn't believe the disease would deal a blow to the province's salmon farming industry.
"I see this as part of reality," he said. "This is a serious issue but the process is in place to manage this."
But Susanna Fuller, a marine co-ordinator at the Ecology Action Centre, said the spread of the disease illustrates the dangers of the farmed fish sector.
"The outbreak brings home very close to home the risks of this industry," she said in an interview.
"This is the kind of thing that happens when we have a high density of fish being farmed in a small area."
Fuller said her group believes the open-pen systems used by Cooke Aquaculture should be discouraged in favour of closed pens.
"We need to be able to do aquaculture sustainably," she said. "Closed-pen systems don't have disease transfer and don't use pesticides and they treat their waste."
A spokeswoman at Cooke Aquaculture did not return a call for comment.
Infectious salmon anemia poses no threat to human health or food safety, but it can kill up to 90 per cent of the salmon it infects, depending on the strain.
The Canadian Food Inspection Agency said the Shelburne Harbour fish farm will remain under quarantine until all fish have been removed and all pens, cages and equipment have been cleaned and disinfected. The process could take months to complete.
The virus first appeared at fish farms in Norway almost two decades ago, then in New Brunswick and later Scotland.
In the late 1990s, New Brunswick salmon farmers slaughtered more than a million fish amid an outbreak. The federal government paid out tens of millions of dollars to settle compensation claims.
The virus was discovered in farmed Nova Scotia salmon as early as 1999, but in much smaller numbers.