Typhoon Wipha caused landslides and flooding on Izu Oshima island, south of Tokyo, with several houses destroyed.
Many people died when their homes collapsed or were buried in mudslides on the island. Two were found dead near a river.
In Tokyo, flights were cancelled, bullet train services suspended and schools closed.
“It is the strongest typhoon in 10 years to pass the Kanto [Tokyo area] region,” Hiroyuki Uchida, the Japan Meteorological Agency’s chief forecaster, told journalists on Tuesday.
The storm brought strong winds and record rainfall – 4.8 inches in one hour on Wednesday morning – to Izu Oshima island, which lies some 75 miles south of Tokyo.
Officials on the island said that 13 bodies had found and more than 50 people were unaccounted for.
“We have no idea how bad the extent of damage could be,” town official Hinani Uematsu said.
Local media described mud and debris strewn around houses.
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