The man's death was reported by the province on Friday. It is the first recorded fatality since 2000.
Officials said he caught the virus after sweeping up mouse droppings at a cottage.
Manitoba's medical officer of health confirmed the hantavirus link on Friday.
"This time of year a lot of people are getting the flu so it's easy to miss [hantavirus]," Dr. Richard Rusk said. "But there was a history of having been exposed to mice droppings."
Health officials are urging people to wear gloves and masks when working around or cleaning out areas where there may be mice.
The hantavirus infection, also known as hanta virus pulmonary syndrome (HPS), is a very rare viral disease which can be fatal.
Early symptoms of hantavirus infection include fever and muscle aches, possibly with chills, headache, nausea, vomiting, diarrhea, abdominal pain and cough, which progresses to respiratory illness, the province said in a release.
The symptoms develop within one to six weeks after exposure to deer mouse droppings.Suggest a correction