The typhoon forced airline companies to cancel more than 140 flights, affecting more than 10,000 passengers.
Ninomiya Ferry services were also suspended, public broadcaster NHK said.
About 1,600 homes in the typhoon-hit region were without power as of Thursday morning, Kyodo news agency said.
Meanwhile, the Japan Meteorological Agency issued a tsunami warning after a strong quake hit near Sakhalin island in Russia's east.
The quake, with a preliminary magnitude of 6.4, struck at 11:38am (02:38 GMT) near southern Sakhalin, according to the meteorological agency.
Russian news service Interfax said one person died in the quake.
Tsunami waves of about 20cm hit the coastal town of Rumoi on Japan's northernmost island of Hokkaido shortly after 1pm.