Typhoon Phanfone made landfall at the city of Hamamatsu, central Japan, shortly after 8 am (2300 GMT Sunday), the Japan Meteorological Agency said.
About 2.7 million people had been advised to evacuate their homes, but most of the advisories were lifted, the Kyodo News agency reported.
The weather agency was still warning of mudslides, swollen rivers and strong winds in some areas of the country.
Tens of thousands of households lost electricity in eastern and central Japan, while rainfall reached 87 millimetres per hour in the city of Shizuoka.