Public Safety Canada says travellers will be able to apply within two weeks for unique codes intended to prevent no-fly list mismatches.
The "Canadian Travel Number" is a key step in revamping passenger-screening procedures after many young children were stopped at airports because their names were the same as, or close to, ones on Canada's no-fly roster.
Passengers who have experienced difficulties will be able to apply for a travel number via the Public Safety website to help avoid false matches when booking flights to, from or within Canada.
The airline would give the number to the government, which will be responsible for screening passengers against the Secure Air Travel Act watch list, commonly known as the no-fly list.
Federal officials would then inform the air carrier should there be any added screening requirements or an outright prohibition on allowing the person to fly.
The government says the new system will improve the security of air travel and protect passenger privacy since airlines, which now use the no-fly list for screening, will no longer have direct access to it.