A shepherd in western Vorarlberg province, who had checked into hospital in July with flu-like symptoms, was found to have the illness following a blood test.
But the man said he had noticed no tick bites, the usual method of transmission, two experts from the Institute of Virology at Vienna Medical University wrote in an article published Thursday.
Doctors finally traced the cause of the illness to the cheese, which the shepherd had made from unpasteurised goat's and cow's milk on an isolated pasture at over 1,560-metre (5,120-feet) altitude.
Three other members of his family, who had not been on the pasture, also exhibited flu-like symptoms and headaches.
Further tests found that one of the goats, whose milk had been used to make the cheese, as well as other animals who had eaten leftovers, had developed TBE anti-bodies, meaning they had also been infected.
Ticks were believed until now to be found only below 1,350-metre altitude, but this may have changed due to global warming, the experts said.
Cases of TBE infections via dairy products were reported in recent years almost exclusively in Baltic countries.