The RCMP said the aircraft left Scott Lake, Sask. Thursday at 7 p.m. CST and was reported overdue at about 1 a.m. Friday.
"A plane went down right across the border," said Cpl. Barry Ledoux with the RCMP. "So a search was initiated so we called the joint coordination center at the Trenton, Ontario who put a team together and send in a Hercules aircraft."
The plane was found about 80 kilometres northwest of Stony Rapids, Sask. on the North Territories side partially submerged in an Ivanhoe Lake.
A dive team from Regina will be sent to the crash site Saturday.
The pilot was the only person on the plane. His name has not been released.
Officials said the aircraft belonged to Transwest Air based in Prince Albert, Sask. No one from the company was available for comment.
Check CBC News for more details on this story as they become available.