The agency says the farm is under a strict quarantine as the CFIA establishes movement controls and helps nearby farms with enhanced biosecurity measures.
This is the second Ontario farm that has the highly pathogenic H5N1 strain of avian flu that has spread around Europe and the United States in both wild and commercial birds.
Meanwhile, the discovery of a red tailed hawk with bird flu in Waterloo, Ont., last week has prompted the Toronto Zoo to close its aviary to the public.
It says the measure is to prevent bird flu from gaining hold among its birds. The zoo says only staff will have access to the aviaries at the moment.
There have been bird flu outbreaks at commercial and non-commercial farms in Nova Scotia and Newfoundland and Labrador in recent months.
The agency says avian influenza is not a significant public health concern for healthy people who are not in regular contact with infected birds.
It says people should stay away from any birds that appear to be sick and call them or a local veterinarian with any concerns.