The case was discovered by the Canadian Wildlife Service in a live thick-billed murre on Coats Island in mid-July.
The territory says testing of the bird recently confirmed the case.
Avian flu has been discovered in birds in all of Canada’s provinces, as well as in Yukon.
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While highly contagious among birds, the risk of avian influenza infection to the general public is considered low.
Residents who hunt wild birds and harvest eggs are advised to wear gloves, wash their hands, and clean their clothing and equipment.