Typhoon Goni slammed into the Japanese mainland on Tuesday, leaving 13 people with minor injuries and disrupting rail and flight services, as the government issued an evacuation advisory for more than 100,000 residents.
The powerful storm, which killed at least 26 people in landslides and floods in the Philippines, hit southwestern Kumamoto prefecture at about 6:00 am (2100 GMT Monday), Japan's weather agency said.
Most of those injured sustained minor cuts from broken glass, a prefectural official told AFP.
Packing gusts up to 198 kilometres (123 miles) per hour, Goni was moving just north of Kyushu, one of Japan's four main islands, the Japan Meteorological Agency reported, as it warned residents to expect violent winds, floods and high waves.
Local governments in northern Kyushu and other prefectures on the main island of Honshu issued evacuation advisories for more than 100,000 people, public broadcaster NHK reported.
Most regional railway operators halted operations, while scores of flights arriving and departing from local airports were also cancelled, including international services between major city Fukuoka and other regional centres including Seoul and Shanghai.
At 10:00 am local time (0100 GMT), about 425,000 households in Kyushu were left without electricity after blackouts, said a spokeswoman for Kyushu Electric.
At the weekend, Goni hit parts of the northern Philippines hard, destroying nearly 1,000 houses and forcing more than 12,000 people to flee, the country's civil defence office said.
More than a dozen people in the mountainous region were killed by landslides, surging waters and a falling tree.
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