Typhoon Jongdari is currently packing winds of nearly 200 kilometres (125 miles) an hour, Japan's Meteorological Agency said, and local media reported the system would hit the country's main island on Saturday night.
Authorities are warning of heavy rain, landslides, strong winds and high waves, and urging people to consider early evacuation.
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On Friday, the storm was about 1,200 kilometres southwest of Tokyo, heading towards Chichijima Island, but it is expected to barrel towards the western Chugoku region by late Saturday.
The region was hit earlier this month by devastating record rainfall that caused flooding and landslides that killed around 220 people.
It was Japan's worst weather-related disaster in decades, and many residents of affected areas are still living in shelters or damaged homes.
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Many became trapped in rising flood waters after failing to evacuate despite orders to do so, and officials Friday urged people to take evacuation warnings seriously.
"Some people failed to evacuate after the recent heavy rain, believing they would be fine," a weather agency official told AFP.
Japan is now in typhoon season, and is regularly struck by major storm systems during the summer and autumn.
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