
Typhoon Shanshan was expected to cross the Amam island area on Wednesday, packing gusts of up to 215kph before veering towards the main southern island of Kyushu.
Typhoon Ampil disrupted hundreds of flights and trains this month, dumping heavy rain but causing only minor injuries and damage as it churned up the Pacific coast past the Tokyo region.
That system came days after Tropical Storm Maria dumped record rains in northern areas of Japan.
Typhoons in the region have been forming closer to coastlines, intensifying more rapidly and lasting longer over land due to climate change, according to a study released last month.