Vancouver Island District RCMP spokesman Darren Lagan said the 55-year-old pilot and a 43-year-old passenger survived the crash with serious injuries.
Both are residents of southern Vancouver Island.
Police said the Transportation Safety Board has been advised.
The lone, uncontrolled runway at the Duncan Airport remained closed Saturday due to the location of the wreckage and the presence of emergency crews, police said.
The cause of the crash has not yet been determined.