About 230 people work at the three plants.
The one in Sydney, Nova Scotia, will close in June and the one in Princeville, Quebec, in August.
The plant in Ottawa will remain in operation until December, 2017.
Saputo owns a total of 54 plants around the world, most of them cheese plants in Canada and the United States.
Last year it bought a major dairy business in Australia and it also has a major dairy business in Argentina.