The storm came less than a week after Typhoon Lan left five dead, one missing and scores injured.
Saola was moving 60 km southwest of Okinawa's capital Naha at 11 am local time, packing gusts of up to 162 km per hour, Japan's weather agency said.
The storm is set to pass through Okinawa and the small subtropical island chain of Amami, which lies between Okinawa and Kyushu, later this evening and then hit southern Kagoshima prefecture tomorrow morning.
Large storms regularly strike Japan, with 22 people killed when Typhoon Lionrock pounded the country last September.
In August, Typhoon Noru killed two people and injured 51.
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