The Port Wade aquaculture sites in the Annapolis Basin, Shelburne Harbour and Jordan Bay are reporting mortalities.
"A department fish health veterinarian has visited the sites in Port Wade and Shelburne and will visit the Jordan Bay site in the next few days to investigate the expected cause of death," said Fisheries and Aquaculture Minister Keith Colwell.
"Our provincial fish health veterinarians investigate mortality events to rule out diseases of concern."
A preliminary investigation has found that a superchill happened.
Most winters, Nova Scotia's marine waters stay above freezing. Sustained cold air temperatures can drop the water below 0 Celsius, to the temperature that fish blood freezes, around -0.7 C.
Tides in late February and early March also tend to be high, and contribute to lowering temperatures in sea cages by flooding more shallow areas than usual. Low air temperatures cool the water and receding tides flush the cages with superchilled water.
The events happen every five to seven years.
The deaths do not pose any risk to the environment. The company has been speaking with community liaison committees.
The operator has been properly disposing of the dead fish.