The provincial government said coastal waters typically remain above freezing during the winter, but every five to seven years cold air can cause shallow ocean water to drop below -0.7 C, the temperature at which fish blood freezes.
The government says in two cases, net pens were damaged and dead fish were released, but the nets have since been repaired and there is no evidence that live fish escaped.
Fisheries and Aquaculture Minister Keith Colwell said it's still not known exactly how many fish have died, but the dead fish have been removed and properly disposed of. He said at least one pen suffered a total loss.
Colwell said the rare act of nature is unfortunate and the department will continue to monitor the situation.
"This is a very unusual case and it's not something we expect to repeat itself in the future," said Colwell. "There's really nothing the company could have done or we could have done to prevent this. It's just a weather condition."
Colwell said the extreme cold also killed wild mackerel in Bras d'Or Lake in Cape Breton.
The sites, operated by New Brunswick's Cooke Aquaculture, are at Shelburne Harbour, Jordan Bay and Port Wade.
Note to readers: This is a corrected story. A previous version based on information provided by the Nova Scotia government said mackerel were among the fish that died at the aquaculture sites.