Authorities urged at least 350,000 people to leave their homes.
Typhoon Nangka hit the island of Shikoku, bringing torrential rain and winds of up to 115 mph.
Kyodo news agency reported at least two deaths while broadcaster NHK said at least 31 were injured.
Nangka has since weakened and been downgraded to a tropical storm, but officials have warned of continued strong winds and storms in the area.
As of July 17, the Japan Meterological Agency warned of high waves, gales and thunderstorms in many parts of the main island of Honshu, as the storm headed north.
Typhoon Nangka is currently moving slowly at 10mph with a maximum sustained wind speed of 60mph, according to the Japan Meteorological Agency.
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