The Canadian Food Inspection Agency has ordered Cooke Aquaculture to destroy salmon in their ocean pens outside Shelburne Harbour due to the presence of infectious salmon anemia.
Outbreaks of the disease in New Brunswick in the late 1990s dealt a blow to the industry there at the time and the federal government provided tens of millions of dollars in compensation.
But Nell Halse, a spokeswoman for Cooke Aquaculture, said Friday her company doesn't believe the virus will spread beyond the one site where it's been detected — and the firm intends to proceed with applications for two new sites in nearby Jordan Bay.
Halse said companies learned from the New Brunswick experience, adding that changes in equipment, the rotation of site and increased testing have made disease spread less likely.
"Both government and the industry are moving very quickly to protect the environment, and to protect wild fish as well as farmed fish," she said.
"This is the story of how it should be done and why the Canadian system is working."
Halse said in the late 1990s, fish farms were closer together, and some didn't rotate the use of pens nor disinfect boats. But she said the industry today thoroughly disinfects areas where the virus is found and divers must change their equipment before going into a new site.
Cooke will not be putting fish in a nearby operation in Shelburne harbour this spring, and no fish will be returned to the closed site until the spring of 2013, she said.
She added that the 13 other sites in the province — including 10 Cooke Aquaculture owns — are distant enough to make transmission unlikely, though she acknowledged there is always a risk of wild salmon spreading the virus.
The company will apply for compensation through a federal program, but Halse declined to say how much it is asking for because Cooke Aquaculture is a private company.
Susanna Fuller, a spokeswoman for the Ecology Action Centre, said the industry is in a constant battle to prevent spread of the disease.
"Everywhere it's happened, whether New Brunswick or Chile, it has spread site-to-site," she said.
She said she is also opposed to Ottawa's practice of compensating the industry for fish lost to disease.
"They've compared it to farming," she said. "But this is an industry that doesn't treat its own sewage ... and it already is getting a significant break."
Halse said as a result of the kill order, the fish at the farm in question will be hauled into a vessel and put through a mechanized system that delivers a blow to their heads before they're sent to be composted.
The provincial Fisheries Department said in an email that it is reviewing Cooke Aquaculture's expansion plans.