The CFIA’s website says the disease was confirmed Saturday in the Rural Municipality of Whitemouth, east of Winnipeg.
The infected premises has been placed under quarantine and the CFIA says it will be establishing movement control measures on other farms in the area.
The agency says the disease was also confirmed in Rocky View County in Alberta on Saturday.
Last week the Manitoba government announced two cases of avian influenza had turned up in two separate wild bird samples in Manitoba.
Manitoba Natural Resources and Northern Development said one sample came from snow geese in Waskada, and the other from a bald eagle near Dauphin.
Although officials say the risk of transmission of avian influenza to humans is low, they warn that people should not touch dead birds or other wildlife with their bare hands.
Anyone spotting clusters of six or more dead waterfowl, any number of dead raptors or scavengers, like ravens or crows, or any larger groups of dead birds is asked to contact the province’s tip line at 1-800-782-0076, as investigations continue.
— with files from Sam Thompson