Typhoon Etau brought winds of up to 78mph to central Aichi prefecture on September 9 before moving out to sea.
Heavy rain continued to drench eastern Japan on September 10.
“This is a scale of downpour that we have not experienced before. Grave danger could be imminent,” the chief forecaster at the Japan Meteorological Agency, Takuya Deshimaru, told an emergency press conference.
The hardest-hit area on September 10 was north of the capital, in Ibaraki and Tochigi prefectures.
The Fire and Disaster and Management Agency said one person is missing and 15 others had been injured, two seriously, both of whom were elderly women knocked over by strong winds.
Local media has reported one person missing after a landslide hit a house in Kanuma, Tochigi prefecture.
Some areas had power outages and parts of Tokyo saw flooding as authorities on September 10 advised about 900,000 people in the capital and other parts of the country to leave their homes.
The extreme weather also disrupted transport links, with dozens of flights cancelled and bullet train services partially suspended.
Last month, powerful Typhoon Goni hit Japan’s southernmost main island of Kyushu, killing at least one person and injuring 70 others.
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