Tropical storm Shanshan, currently moving over southwestern Japan, has killed at least four people and injured more than 90.
Three people died in the central prefecture of Aichi after rainfall triggered a landslide, which struck a house.
Crews managed to rescue two people from the rubble.
In Tokushima Prefecture, a man in his 80s died when the roof of his house collapsed.
Officials in Miyazaki prefecture say they have received over a hundred reports of damage caused by wind, including from at least one tornado that touched down.
Tropical storm Shanshan is disrupting travel including on some of Japan’s busiest rail lines as it continues along a northeastern path.
Services on the Tokaido Shinkansen bullet train between Tokyo and Osaka were suspended on Thursday. Services between Osaka and Nagoya resumed Friday morning, although operations from Nagoya to Tokyo will remain suspended throughout the day.
Hundreds of people stranded by the storm were forced to make alternative sleeping arrangements. The bullet train operator set up so-called “train hotels” at stations in Tokyo, Shin-Osaka and Nagoya.
Further west, services on Shinkansen lines linking major cities including Hiroshima and Fukuoka remain suspended, along with all bullet train services in Kyushu.
Major air carriers, including All Nippon Airways and Japan Airlines, have cancelled hundreds of flights.