Darren Spence, 37, was the pilot of the plane that was carrying his sons, Logan, 10, and Gage, 9. The third boy on the plane, a friend of the brothers, was also nine.
There was no one else aboard the aircraft, police said.
Waskada Mayor Gary Williams said all the victims are from the village, which has been devastated.
"We know them very well. It's …, yeah, well it's the worst thing that anybody can imagine," he said.
"It's just a very difficult situation and, I don't know, this is going to be the start of just a really hard week. Hope our community can pull together."
Williams called Spence "a good friend … [and] a good father. He was a guy that could brighten your day when you met him."
Counsellors and mental health workers are at the school where the three boys attended. The school only has about 100 students and everyone knew each other, Williams said.
Spence was an experienced pilot and it wasn't unusual for him to take people up for a short flight, Williams said, adding the weather was fine.
The RCMP's Killarney detachment was notified of an overdue Cessna aircraft around 6 p.m. Sunday, and the small plane was found in a field about an hour later.
It was located about 10 kilometres north of the village after Canadian Forces search and rescue technicians were dispatched to the area.
Transportation Safety Board of Canada regional manager Peter Hildebrand told reporters the six-seat Cessna 210C had departed at around 1 p.m. from a private airstrip in the Waskada area, en route to Brandon.
Hildebrand said an emergency beacon from the plane was spotted at CFB Trenton at about 1 p.m. but the search didn't start until 6 p.m. when RCMP were informed the flight was late.
It's not uncommon for such delays because the beacon was an old-style one that goes off on impact but doesn't have GPS, so there's no way to know where a plane has gone down, only that it has, he said.
Once emergency officials have a rough location of the crash they can begin the search.
The crash site was discovered at 6:35 p.m. in a farmer's field, Hildebrand said.
RCMP Forensic Identification personnel and Transportation Safety Board officials are on scene investigating.
Hildebrand said investigators have not had a chance to look at the aircraft's maintenance records yet.
The village of Waskada is in southwestern Manitoba near the U.S. border.