In September and October last year the agency tested 165 sports nutrition and fortified food products on sale in retail stores in Canada and found that 117 contravened composition, nutritional information or labeling requirements.
The laboratory reports were not initially released to the media but made headline news this week when they came into the public domain after being requested under the general access to information law.
The media interest has sparked a strong response from some of the companies whose products were shown not to comply with regulations.
Jamieson Laboratories issued a statement saying claims that its Jamieson Slim Down Bars are non-compliant are "wrong, premature and irresponsible".
The company said is involved in ongoing discussion with the CFIA over its method of testing for vitamin A, which does not show microencapsulated vitamin A in its bars.
"Jamieson is outraged that information linked to a report that is both flawed scientifically and inconclusive is being circulated as fact," says Gary Leong, VP of scientific and technical affairs.
"The microscope should be squarely pointed at federal regulators and their ineffective methods rather than nutritional supplement and meal replacement manufacturers."
But according to CFIA spokesperson Marc Richard the testing methods were circulated to companies in advance, and that it was up to them to meet the requirements according to the methodology. He called it "an open book exam".
Richard added that the quality of the science could not be called into question as the tests were carried out in food and pesticide laboratories that have been ISO certified since the mid 1990s.
Not all the makers of products tested are disputing the methodology and results, however.
Nestle Canada, the maker of Powerbar, which was found to comply with regulations, has spoken out in support of CFIA's initiative, saying that it will "rid the marketplace of products with illegal ingredients and claims".
"This will ensure that only products that are in compliance with regulations are available to Canadian consumers."
Richard told NutraIngredients-USA.com that the main aim of the investigation was to educate manufacturers and retailers of a relatively new group of products about regulations contained in the Food and Drug Act and the Consumer Packaging and Labeling Act.
It follows the publication in June 2002 of an open letter to retailers, manufacturers and importers of sports nutrition products informing them of requirements.
Whilst Richard was not able to confirm what action, if any, the CFIA was taking over violating products, he played down the significance of the report to public health.
"If there were immediate health concerns there would have been news releases."
Nonetheless the inspectors saw fit to detain or destroy a total of 15 failing products. The identity of these has not been made known.
In the majority of cases, non-compliance with Canadian regulations was due to labeling issues, especially in products imported from the United States. More detail is required on the nutritional facts panel for products sold in Canada than in the US, and information must be given in both English and French.