Transport Canada says the new technology, already in use in the U.S. and the Netherlands, will increase privacy while still ensuring security.
The scanners have been in use at Canadian airports for three years and there now are 52 of the devices installed across the country.
They work by beaming low-level radio frequency energy over and around the passenger's body.
Instead of a silhouette of a person's physique, the new software will produced a stick figure on the scanner's screen and identify areas of the body where objects might be concealed under clothing.
Transport Canada says the scans can identify anomalies on a passenger, including metals and non-metals of all shapes and size; ceramic-type threats such as knives and sharp instruments; liquids and explosives.
The department stressed that the scanner does not collect personal information from the passenger, nor is the image correlated in any way with the name of the passenger or any other identifying information.
Steven Fletcher, minister of state for transport, said the new technology is good news for air travellers.
"This new software will ensure the continued safety and security of Canadian passengers, while respecting their privacy," he said in a news release.