The Royal Canadian Mounted Police said the plane went down near the hamlet of Resolute Bay in the Arctic territory of Nunavut.
The First Air charter flight, No. 6560, was traveling from Yellowknife in the Northwest Territories to Resolute Bay and was scheduled to continue on to Grise Fiord on Ellesmere Island.
RCMP Constable Angelique Dignard said 12 people died in the crash and three people were injured. The plane was carrying 15 people, including four crew members.
Two adults and a child were flown to a hospital in the territorial capital of Iqaluit for treatment, police said. One of the adults was in critical condition.
First Air said in a news release that the plane last reported communication at 12:40 p.m. local time when it was about five miles from Resolute Bay airport.
The crash site is less than 1.2 miles west of the Resolute Bay community and is in rough terrain accessible by all-terrain vehicles, Dignard said.
Resolute Bay is an Arctic waterway in Nunavut. The population of the hamlet is about 230, many of whom are aboriginal natives known as Inuit people. But hundreds of military personnel were in the region to take part in the Canadian military's annual northern training exercise, Operation Nanook, next week.
Chris Krepski, spokesman for the Transportation Safety Board of Canada, said it was too soon to say what caused the crash.
Krepski said investigators were already in Resolute Bay for the military exercise and arrived on the scene soon after the crash.
Witnesses said the plane crashed into a small hill near the airport runway. Local residents rushed to the site on their ATVs to see if they could help.
"You could see parts of the plane everywhere . . . tail, nose, everything," said Saroomie Manik, a former mayor of the community who went to the site.