The centres, expected to be implemented over the next few years, will consolidate and co-locate expertise for specific programs.
CFIA said the move will create a more efficient system for providing guidance and expert advice and a stronger link between the people who design policy and programs and the staff who deliver them.
The agency said it considered current concentration of related industries, proximity to industry organizations, proximity to provincial and academic experts in that field and current concentration of staff involved in the activity.
Who will do what?
Red meat slaughter and foreign animal disease and emergency management will be managed from Calgary, Alberta.
The National Capital Region will handle labelling and claims and animal feed issues.
Poultry slaughter, processed meat and poultry and domestic animal disease and animal welfare will be focussed at St-Hyacinthe, Quebec.
Shellfish and aquatic animal health will provide shellfish and aquatic animal health expertise and advice.
Industry and stakeholder link
CFIA said the move builds on the efforts to improve how it interacts with stakeholders and improve industry's understanding and compliance with federal regulations.
Gerry Ritz, Canadian agriculture minister, announced that the Centres of Expertise will provide industry and CFIA inspectors with better, more consistent access to information and advice.
"These Centres of Expertise will pool expertise and make it available through a single window, making the CFIA more efficient and giving industry, CFIA inspectors and Canadians better, more consistent service," said Ritz.
"In addition, locations will be near both academic and provincial experts in a particular field to leverage expertise and collaboration among organizations."
Last year Canada was hit by an E.coli O157 outbreak from beef from XL Foods which led to thousands of products being recalled and 18 cases being reported.