"A novel non-pandemic influenza A virus has been confirmed in two hog farm workers in Saskatchewan and a third case is under investigation," the provincial authorities said, noting the workers had fully recovered.
Health Minister Leona Aglukkaq said: "We are working closely with the province of Saskatchewan to learn as much as we can about this new flu virus.
"Preliminary results indicate the risk to public health is low and that Canadians who have been vaccinated against the regular, seasonal flu should have some immunity to this new flu strain," she added in a statement.
The Public Health Agency of Canada (PHAC) said its microbiology lab in Winnipeg, Manitoba had found that the new strain consisted of genes from human seasonal flu and swine flu viruses.
However, it stressed, the virus was not a new strain of the pandemic A(H1N1) flu virus that first emerged in Mexico in late April before spreading across the world.
"There is no evidence," PHAC said, "that this new human strain of the virus is present in the swine herd."
Worst hit by the A(H1N1) virus are the United States with 170 deaths, Mexico (119 deaths) and Argentina (60 deaths), ahead of the 37 people killed by the pandemic in Canada.
The World Health Organization has also been informed of the new strain in Canada.
Striking a reassuring tone, local health officials stressed that these types of viruses are not easily transmitted between humans and that there was no evidence to the contrary.
"Our ongoing surveillance detected the new strain, and we will continue to aggressively monitor and test Saskatchewan residents in the affected area," said the province's chief medical health officer Moira McKinnon.
Saskatchewan said it had taken several precautionary measures, including boosting surveillance of humans and pigs, reinforcing bio-security on the hog farm, which was not identified by name, and vaccinating the farm's workers.