A precautionary quarantine was put in place at the unnamed commercial facility after the possible discovery of infectious salmon anemia.
The agency says further disease control measures will be put in place and the World Organisation for Animal Health will be notified, if anemia is confirmed.
Officials say it's not clear what those measures could be since it is early in the investigation.
In July, a salmon farming operation in St. Alban's, N.L., owned by Grey Aquaculture, was quarantined and the fish destroyed after an outbreak of the disease.
Last week, Liberal Fisheries critic Jim Bennett raised concerns about ocean farmed salmon, suggesting the industry adopt inland tank farming techniques.