Typhoon Talim made a landfall in Kyushu, the southernmost of Japan's four main islands, packing winds of up to 162 kilometres per hour, the Japan Meteorological Agency said.
At least 644 domestic flights have been cancelled because of strong winds, according to public broadcaster NHK, while all major regional train services have been suspended, operator JR Kyushu Railway said.
Authorities have issued warnings of rainstorms, high seas, possible landslides and flooding across the southern half of the Japanese archipelago.
The meteorological agency said the typhoon was expected to head northwards, dumping heavy rain across a large area, including on Tokyo.
Big storms regularly strike Japan, with 22 people killed when Typhoon Lionrock pounded the country last September.
Last month, Typhoon Noru killed two and injured 51.
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