The infection was caused by an H1N1-variant virus, which is not the swine flu virus that has been jumping from pigs to people in the United States this summer.
That virus, an H3N2-variant, has caused 305 infections this year in the U.S. but has not been spotted in Canada to date. Most infections with the H3N2-variant flu have been in people who visited pig barns at state and county fairs.
Dr. Arlene King, Ontario's chief medical officer of health, said the man is being treated in a hospital in southwestern Ontario. She did not indicate whether that is as a precaution or because he is seriously ill.
"It's likely an isolated occurrence," she said.
The man worked with pigs in both Canada and the United States, but it's still unclear where he may have picked up the new virus, she said.
The new virus is one that rarely spreads from animals to people, and human-to-human spread is also rare. So far, none of the man's family or friends are showing signs of illness, King said.
She stressed the discovery of the infection does not trigger food safety concerns. "Proper cooking of meats, including pork, kills all bacteria and viruses."
She also urged people to remember that hand washing and getting a flu shot are the best way to protect against contracting the flu.
The term variant is added to flu virus names when viruses that normally circulate in animals cause infections in humans. In written form it is often shortened to a "v" at the end of the virus's name.
This H1N1v virus would be a distant cousin of the H1N1 viruses that have been circulating in people for most of the last century. That family includes the virus that cause the 2009 pandemic.
But viruses within a large family group such as H1N1 can be sufficiently different from one another that antibodies to one won't fully protect a person from becoming infected with another.
U.S. authorities have also seen one case of infection with an H1N1v virus there this summer, in Missouri.
King could not say whether the genetic blueprints of the Ontario and Missouri viruses were closely related. Genetic sequencing of the Ontario virus is still being done, so they haven't had a chance to compare it to the one spotted in Missouri, King said.
She said they do know it contains the M gene of the pandemic H1N1 virus, which is also present in the swine flu viruses that have been causing human infections in the U.S. this summer.
Scientists suspect it may make it easier for swine viruses to infect people, but that hasn't been proven.