Staff and shoppers began smelling a strong chemical odour around 6 p.m. local time, and some people started coughing.
The Iqaluit Fire Department was called, and staff evacuated the store of about 60 people.
Two fire trucks and about 20 firefighters responded.
Lt. Chris Wilson said they put on their safety equipment "and we basically began to investigate,” he said.
“We also ventilated the building. And my crews found a can of pepper spray that we feel was activated. We have no idea if it was accidental or intentional. But that's now what we suspect was the issue ... some sort of bear spray."
By about 7 p.m., store managers were allowed back in and firefighters were already preparing to leave.
Wilson said the bear spray that was activated was not being sold — it was not on one of the store shelves or in the stockroom, it was behind one of the store's counters.
He said it's not clear if it was set off accidentally or intentionally but that he doesn't think it was set off by a member of the public, or set off maliciously.