Typhoon Nari was located 350 kilometres northwest of Amami-Oshima island at 5:40 pm (0840 GMT) and moving north at 20 kilometres per hour, the meteorological agency said.
Nari, which means "lily" in Korean, is expected to bring heavy rain to southern Japan and the Korean peninsula, with the national weather agency issuing warnings of possible strong winds and high waves.
At least two people were lightly injured by broken window glass on Kume Island, Okinawa prefecture, a local firefighter said.
Japan and other nations in the western Pacific are hit each year by lethal typhoons. Earlier this month, Typhoon Fitow hit eastern and northern Japan, killing at least two people and injuring 82 others.