Nunavut's Environment Department is investigating the deaths of two polar bears near Pangnirtung earlier this month.
Both bears drowned after they were tranquillized by researchers doing an inventory of bears in the Davis Strait.
Steve Pinksen, director of policy with Nunavut's Environment Department, told CBC News that researchers have occasionally killed bears in self-defence, but it's very rare for a bear to die after being tranquillized.
Pinksen said he believes the latest cases were the third and fourth deaths in the past 25 years of research, in which thousands of bears have been darted.
"In most communities, they don't particularly like us to handle bears. And, really, we don't like to handle bears either. It's a necessary step," Pinksen said.
"I'd hope that in the long run people see the value, that we really need the information from the research and there will be some cost to that… including the odd dead bear."
Pinksen said researchers jumped into the water to try and keep one of the bears, a large male, from drowning. However, the bear was too large.
The bears will be taken from the Pangnirtung area's polar bear hunting quota, Pinksen said.
The environment department will pay the local hunters and trappers association $5,000 for the hide from each bear, as well as $300 for the meat.