The Harper government is deploying Automatic Target Recognition (ATR) software on the existing scanners at major airports across the country, he said.
“This new software will ensure the continued safety and security of Canadians passengers, while respecting their privacy," Fletcher said in a statement.
The software produces a stick man image rather than a three-dimensional outline of a passenger's body, he said.
The current scans have come under fire as being too revealing.
Earlier this year, the U.S. Transportation Security Administration announced its X-ray scanners will be removed from airports this summer because the company that makes them can't resolve privacy concerns raised about the 3D images.
U.S. Congress had ordered that the scanners either produce a more generic image or be removed by June. The manufacturer, Rapiscan, acknowledged it wouldn't be able to meet the deadline.
As a result, the U.S. is also applying the ATR software to scanners.
The millimetre-wave technology projects low-level radio frequency energy over and around the passenger's body. The radio frequency wave is then reflected back from the body and signals are recovered using sensitive detectors.
A stick figure is displayed on a screen, identifying areas of the body where objects may be concealed under clothing.
The ATR technology is in line with international standards for security screening, said Fletcher, noting the Netherlands also use the technology.
The scanners do not collect personal information from passengers and images are not correlated with the name of the passenger or any other identifying information, he said.
Passengers selected for a secondary search can choose between the full-body scanner or a physical search.
There are 51 full body scanners at 18 airports across Canada.
Full body screening technology has been in use at Canadian airports for three years.