The provincial government says the unnamed site has been in quarantine since late last month, when the presence of infectious salmon anemia was first suspected.
The virus is not considered harmful to humans but is a risk to other fish farms in the region.
The Centre for Aquaculture Health and Development in St. Alban's, N.L., says the case marks the second time infectious salmon anemia has been detected in recent months.
In July, a salmon farming operation in St. Alban's owned by Grey Aquaculture was quarantined and the fish destroyed after an outbreak of the disease.
Officials say they don't believe the two outbreaks are related.
There are 133 aquaculture sites in Newfoundland and Labrador.
The provincial government says aquaculture production was worth $120 million last year.