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Sockeye salmon in a river in the Bristol Bay, Alaska watershed in 2007.Ben Knight/ Associated Press

The Canadian Food Inspection Agency plans to test nearly 8,000 wild and farmed salmon over the next two years to find out if three potentially deadly fish diseases are present in British Columbia waters.

The project is an intensive investigation aimed at detecting any signs on the West Coast of infectious salmon anemia, infectious pancreatic necrosis or infectious hematopoietic necrosis.

"All three diseases are highly contagious, can cause mortality in wild and aquaculture salmon," states a ministerial briefing note prepared by CFIA staff and updated Dec. 8. "Surveillance objectives are to determine the absence/presence of three diseases of trade significance … [and]to support international trade negotiations by making [a]disease-freedom declaration that will stand international scrutiny," states the note, which was filed as evidence recently at the Cohen Commission of inquiry.

A draft copy of the CFIA surveillance plan was also entered at the hearings, which concluded on Monday.

During testimony, Kim Klotins, acting national manager of the CFIA's aquatic animal health division, said the plan is still being worked on, but it should be in place by early next year.

The draft plan states that 7,700 salmon will be collected for sampling over two years, and that nearly 20,000 tests will be undertaken on the fish.

Salmon will be captured on spawning grounds, taken from federal fish hatcheries, caught at sea and collected at fish farms and from commercial fishing boats and processing plants.

The surveillance strategy, which also involves the Department of Fisheries and Oceans and provincial authorities, was developed this year following reports that three laboratories had obtained positive hits for the ISA virus in samples of B.C. salmon. However, none of those positive tests could be repeated in follow-up studies, leaving officials unsure if the virus had been discovered or not – and raising concerns internationally about the disease-free status enjoyed by B.C.-farmed and wild salmon.

Mary Ellen Walling, executive director of the BC Salmon Farming Association, said her organization will fully co-operate with the CFIA study.

But she said fish farmers on the West Coast remain confident their stock will get a clean bill of health.

"If we were seeing the commonly known ISA virus in British Columbia, we would have significant mortalities on the farms. And we don't have large, unexplained mortality, we have good survival," she said in an interview Tuesday.

Ms. Walling said the industry, which mostly raises Atlantic salmon, has been testing fish for 10 years in B.C. without finding any of the suspect diseases except for an isolated outbreak of IHN several years ago.

She said the industry's disease-free tests and the "low mortality on our farms" indicates none of the suspected diseases are present in aquaculture operations.

"When you pair those two pieces together, I think it does demonstrate that we have good control over the health of the fish," she said.

Alexandra Morton, a researcher and fish farm critic, said it is clear more disease research is needed in B.C., but she questioned the credibility of the CFIA. She said the CFIA appears more interested in maintaining Canada's trade status than in protecting the health of B.C. salmon.

"What's gotten lost in all of this is the biological significance of pathogens," Ms. Morton said. "The commercial significance is very well looked after … the CFIA is … making sure commerce continues. But I do not trust them [concerning]the health and welfare of fish."