The short answer is that the rationale for having the federal and provincial governments participate jointly in these kinds of programs was a very destructive, inter-regional competition that existed before the agricultural policy framework, in which certain commodity groups and certain sectors would be very heavily subsidized, and that would force another province to try the same thing.
It was very, very destructive to producer groups and very inequitable to producers across the country. So the decision was made and has been sustained by ministers that it would take a certain number of majority provinces to agree to a change and covering a certain amount of agricultural production.
So the short answer is no, the federal minister can't make these changes; they are genuinely federal-provincial-territorial collaborations, and there is no unilateral movement.