The Canadian Food Inspection Agency has confirmed an outbreak of salmon virus at a commercial Nova Scotia fish farm, but Cooke Aquaculture says that won't stop a $150-million expansion from being built.

"This does not impact our plans," Nell Halse, Cooke spokesperson told CBC News Thursday from the company's headquarters in Saint John, N.B.

"We're still going full steam ahead with our plans for Nova Scotia, for creating new jobs and building a hatchery and a plant and expanding our feed mill," Halse said

The infectious salmon anemia was confirmed by the agency Wednesday after a sample of 13 salmon, weighing about two kilograms each, were tested by the Canadian Food Inspection Agency.

The company confirmed the outbreak was at its Shelburne N.S. facility.

"The release confirms we have a very good system in place for monitoring fish health and for managing it, and it also confirms that the actions we took several weeks ago were the right ones," Halse said.

Though plans will continue with its expansion, the company says its taking the outbreak seriously.

She said the company has dealt with infectious salmon anemia in New Brunswick in the past.

3 cages to be destroyed in total

When the virus was first suspected in February, Cooke voluntarily destroyed two cages of salmon at its Shelburne facility.

The salmon — believed to be in the thousands — were disposed at a rendering plant.

CFIA says it ordered the destruction of a third pen of fish after ISA was confirmed.

Cooke would not say how many fish are being destroyed, nor estimate the value.

"We're just not giving specific details of how many fish, but we have 20 cages on a farm, so it is still a small percentage of the overall production on this farm," Halse said.

Under new federal rules, owners of water-based animals are entitled to compensation when the government orders them eradicated.

The ISA confirmation is sure to renew the debate over aquaculture in general and Cooke's expansion, especially into Jordan Bay next to Shelburne.

The company is currently seeking government approvals for two farms, each holding up to one million fish in Jordan Bay.

Lobster fisherman Ricky Hallett said he does not accept that ISA poses no threat to the lobster fishery.

"In light of the problems found in Shelburne Harbour, there should be no expansion in Jordan Bay," Hallett said.

Others worry about the potential impact on strugging Wild Atlantic salmon.

"It's just more damaging to wild fish," said Lewis Hinks of the Atlantic Salmon Federation. "It's just another nail possibly in the coffin. It causes us great concern no matter how you look at it."

Nova Scotia's fisheries minister said the situation is serious but in hand.

"It's a normal business day, and that these particular incidents are being managed in an appropriate fashion," said Sterling Belliveau.

The Canadian Food Inspection Agency said it will continue to monitor and test the rest of the salmon at the Cooke facility. If more ISA is found, more fish will be destroyed.

With files from The Canadian Press