A mayday call went out from the 20-metre vessel just before 3 a.m. Saturday, advising that the steel landing craft was taking on water.
Cpl. Poppy Hallam says one man escaped as the vessel capsized and was picked up by a zodiac sent from an Alaskan ferry that heard the emergency call.
An RCMP patrol vessel, a Cormorant helicopter from Canadian Forces Base Comox and three Canadian Coast Guard vessels also responded and carried out a search by air and sea, but the two other occupants were not located.
The vessel went down 800 metres from a dock and Campbell River ground search and rescue searched the water using lights from shore in the hope the men may have tried to swim to shore, but to no avail.
RCMP are now investigating the missing persons case.