Typhoon Jongdari made landfall near Ise, Mie Prefecture, southeast of Osaka, early on Sunday morning.
It brought intense rainfall across wide areas but the total rainfall received has been generally less than 150mm in any one place. This is partly due to the rapid movement of the cyclone; it crossed Japan in under 24 hours.
Jongdari took an unusual westbound trajectory across Honshu, staying north of Shikoku and finally crossing Kyushu. Prime Minister Shinzo Abe took the rare step of advising evacuation, particularly for those in western Japan, where flooding killed 224 people and destroyed tens of thousands of homes earlier this month.
Jongdari left at least 24 people injured but no deaths have been reported.
An interesting consequence of the geography of Honshu was that a hot Fohn wind blew into Niigata Prefecture. A Fohn wind is the result of moist air drying out over mountains and descending as a warm and dry blow on the lee side. This led to temperatures rising to close to 40C.
Typhoons typically approach the Japanese archipelago from the southwest, and many follow a southwest-to-northeast course due partly to the effect of the westerly jet stream and anticyclones over the Pacific.
Rain is expected for another day over Kagoshima prefecture in the southern Kyushu. Here, Jongdari is forecast to strengthen slowly over the warm waters, then head towards Shanghai.