RCMP say the single-engine plane crashed into a sloped area near the runway, causing significant damage to the aircraft, at around 1:30 p.m. Saturday.
A 55-year-old male pilot and a 43-year-old female passenger were on board and emergency crews pulled them from the wreckage.
B.C. Emergency Health Services says one patient was taken by air ambulance to Victoria General Hospital, while the other was taken in stable condition by ambulance to Duncan Regional Hospital.
RCMP say both are believed to be residents of southern Vancouver Island and the full extent of their injures is not known at this time.
Investigators say it's too early to speculate on cause but there's no indication that foul play was involved.
North Cowichan and Duncan RCMP remain at the scene and have advised the Transportation Safety Board of the incident.