Typhoon Goni damaged buildings, tossed around cars and flooded streets in Japan's main island of Kyushu before heading out to the Sea of Japan.
The typhoon left at least 26 people injured, no deaths were reported so far. Philippines was stormed by the same storm earlier.
At least 21 people were killed and 15 people still missing in Philippines after the storm.
Air, road and rail traffic has come to standstill after the storm. More than 470,000 households temporarily lost power.
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According to Japan Meteorological Agency, the typhoon is expected to bring heavy rain to western Japan through Wednesday.
Many local authorities issued evacuation orders to residents.