The RCMP's Killarney detachment was notified of an overdue aircraft around six o'clock Sunday evening, and the plane was found about an hour later.
It was located after Canadian Forces Search and Rescue Technicians were dispatched to the area.
RCMP Forensic Identification personnel and Transportation Safety Board officials are on scene investigating.
Police say no further information will be released until after the victim's next of kin are notified.
The village of Waskada is in southwestern Manitoba near the U.S. border.