Capt. Jean Houde of the Joint Rescue Co-ordination Centre in Trenton, Ont. says the plane went down in Lake Kapekun, which is near the Manitoba-Ontario boundary.
A Hercules aircraft was dispatched from Winnipeg when the plane was reported overdue Saturday night, and two search and rescue technicians parachuted into the crash site early Sunday.
Houde say the technicians found the plane submerged in the lake with the pilot's body inside.
Police say the man was from Gimli, Man., and was the only one reported to be on board.
There's no word yet on why the plane went down.
Houde says the man reportedly took off from Gimli on Saturday morning and was on his way to his cottage on Lake Kapekun. But he says the man's friend, who is also a pilot, flew over the cottage later in the day and didn't see the plane.
The friend called authorities, Houde says, and that's when the rescue centre dispatched the Hercules.
Houde says it was dark at the time, but searchers were able to spot the plane's floats sticking out of the water.
"They have night vision goggles, and it was a full moon last night," Houde said.
After locating the pilot inside the upside-down plane, Houde says the technicians spent the rest of the night on a rocky piece of land. There are no roads to the remote lake, he says, and nowhere for a plane or even a helicopter to land, so the technicians had to wait until a helicopter with a hoist could pick them up.
He says an RCMP recovery team arrived at the site Sunday afternoon and their helicopter was able to transport the technicians out.