A man in his 60s tested positive for the virus, marking the first confirmed infection from Shiga prefecture, an official said at a media briefing on Thursday.
Japan's confirmed coronavirus infections rose above 1,000 on Wednesday, when 36 new cases were confirmed, the biggest one-day increase to date. Twelve people have died from the disease, according to the health ministry.
The rapid spread of the outbreak has raised questions about whether Tokyo can host the Olympic Games as scheduled from July 24.
But IOC President Thomas Bach said the words 'cancellation' or 'postponement' were not mentioned during two-day meeting focused on preparations for the Tokyo 2020 Games.
Asked what made him so confident the Games would go ahead, Bach said the IOC and 2020 Games organizers were receiving expert information, including from the World Health Organization.