The 37-year-old pilot was the father of two of the boys, ages 9 and 10. The third child was a school friend, also 9, the Canadian Broadcasting Corp. said. Police withheld the victims' names, CBC said.
All four are from the village of Waskada, in southwest Manitoba, near the U.S. border.
The six-seat Cessna 210C took off from an airport in Deloraine and was headed to Brandon, Manitoba, the pilot's flight plan stated.
Weather was not believed to be a factor, investigators said.
Waskada Mayor Gary Williams said the entire town is devastated.
"We know them very well. It's, yeah, well it's the worst thing that anybody can imagine," he said.
All three boys attended the same primary school, which only houses about 100 students total. Grief counselors were on hand Monday to help classmates and teachers cope with the loss, school officials said.