The provinces are taking over responsibility for rabies programming from the Canadian Food Inspection Agency.
The changes were announced in the 2012 federal budget and implemented April 1.
Rabies remains a federally reportable disease, meaning animal owners, veterinarians and laboratories still have to report suspected cases to the CFIA.
However, the provinces are looking after the collection and submission of rabies samples and response to suspected cases.
For example, Saskatchewan has budgeted $500,000 for a new rabies response program.
Under the program, veterinarians will collect samples from suspect animals and submit them for rabies testing.
The province will handle any response or follow-up required be-cause of a positive test.
The number of cases in Saskatchewan has dropped during the past few years from 34 in 2011 to 24 in 2012 to 13 last year.
The 2013 cases included two cats, five skunks and six bats.
In Manitoba, 21 skunks, two horses, two dogs, one cat, a fox and a raccoon tested positive last year for a total of 28.
That compares to 25 in 2012 and 21 in 2011.
Alberta saw four cases last year: three bats and one dog. There were two cases in 2012 and none in 2011.