It depends. If the CanadaGAP requirements are stricter, then the manual must be followed. If the federal/provincial/municipal/territorial regulations/ legislation are stricter, then the regulations must be followed.
Prevailing legislation SUPERSEDE the requirements in the manual and must be followed.
Example: Some provinces require that one toilet is provided for every 20 employees while the manual requires one toilet for every 35 employees. Therefore, the operation must follow the regulations in their province for one in 20 if it applies to them. The provincial requirement is stricter than the manual; therefore, the operation must follow the provincial requirement.
However, if the manual requires something that the regulations do not, then the manual must be follow.
Example: In Quebec, according to the regulations, potable water parameters allow for 10 Total Coliforms and 0 E. coli. In order to follow the manual requirements, an operation would have to follow the potable water guidelines of 0 Total Coliforms and 0 E. coli.