The Victoria Rescue Co-ordination Centre says it was alerted at about 5 p.m. Thursday that a personal locator beacon had been activated.
Rescuers determined the beacon belonged to the sole person aboard a small boat travelling between the Sunshine Coast community of Egmont and a resort at the mouth of Princess Louisa Inlet, more than 40 kilometres to the north.
A coast guard life boat and two rescue aircraft were dispatched when the missing five metre aluminum vessel could not be contacted.
The crash was discovered a short time later, about 26 kilometres north of Egmont.
The seriously injured boater had to be hoisted from the scene by helicopter and transferred to Powell River, where an air ambulance rushed him the rest of the way to Vancouver for lifesaving treatment.