Typhoon Nanmadol bore down on Japan's southernmost main island of Kyushu on Sunday with the Japan Meteorological Agency (JMA) warning of gales and high waves "like never experienced before".
The 14th typhoon of the season, classified as a super typhoon by the U.S. Navy's Joint Typhoon Warning Center, could bring record rainfall, the JMA said, warning of the risk of rivers overflowing and landslides.
Southern Kyushu could receive 500 mm (20 inches) of rain and wind gusts of up to 250 km (155 miles) per hour on Sunday, while the central Tokai region could get 300 mm (12 inches) of rain, the agency forecast.
High winds caused damage including downing a bus stop in Miyazaki prefecture, southern Kyushu, according to footage carried by public broadcaster NHK.
Railway operators have cancelled trains and convenience store chain Seven-Eleven Japan temporarily shut around 950 stores. Toyota Motor Corp 7203.T said it will idle production at three factories on Monday.
The storm is forecast to curve east and pass over Japan's main island of Honshu before moving out to sea by Wednesday. Heavy rain lashed the capital Tokyo, with operation of the Tozai subway line suspended due to flooding.
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