Typhoon Talim hit Kyushu, the southernmost of Japan's four main islands with winds of up to 105mph, the Japan Meteorological Agency said.
At least 644 domestic flights were cancelled due to strong winds and regional railway services have been suspended.
Warnings have been issued of rainstorms, high seas, possible landslides and flooding across the southern half of the Japanese archipelago.
Some residents have already been evacuated from their homes amid heavy rainfall.
The meteorological agency said the typhoon was expected to head north, bringing heavy rain across a large area, including the capital Tokyo.
Earlier, the typhoon battered the southern Okinawan island chain bringing the most rain seen over a 24-hour period in 50 years on the city of Miyako, before it hit Kyushu.
Japan is regularly hit by big storms, with 22 people killed when Typhoon Lionrock pounded the country in September 2016.