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.
Image source: Wikimedia Commons President-elect Donald Trump celebrated his election victory at the Ultimate Fighting…
Millions of voters across the US chose to return Donald Trump to the White House…
Donald Trump declares victory in the US election as he addresses jubilant supporters in Florida.…
Stocks around the world are rising as Donald Trump appears to be on the cusp…
Donald Trump has won Pennsylvania, North Carolina and Georgia and taken a lead over Kamala…
Quincy Jones, the celebrated musician and producer who worked with Michael Jackson, Frank Sinatra, Ray…