This info is direct from the Transport Canada site. It appears online or by mail are the only ways.
Small Vessel Register
This registry only applies to commercial (non-pleasure) vessels that are 15 gross tons or less.
This type of registration is required for:
vessels less than or equal to 15 gross tonnes used for commercial purposes with propulsion motors of 10 horsepower (7.5kW) or more (if unsure of tonnage, check this explanation of tonnage measurements)
commercial river rafts
government-owned vessels with propulsion motors of 10 horsepower (7.5kW) or more
This type of registration is not required if:
your vessel does not or will not have a mortgage
you do not wish to register an “official” name
you don’t intend to travel outside of Canada
Register your vessel using the Small Vessel Register either through the online service or by mail using the Small Vessel Register Registration Forms.