There were still more than 50 people missing as the typhoon moved up Japan's east coast, according to local authorities.
Hundreds of flights were canceled and 20,000 people evacuated from their homes in what is being dubbed a "once in a decade" typhoon.
Izu Oshima island bore the brunt of the storm, which brought record rainfall of 4.7 inches per hour and saw houses washed away by swelling rivers.
A mountain on the island reportedly caved in due to strong rains, according to NBC News.
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PHOTO: Houses on Oshima island, south of Tokyo, are seen buried by landslides after Typhoon Wipha grazes Japan pic.twitter.com/zXOVuFs5PW
— Agence France-Presse (@AFP) October 16, 2013
Further north, Tokyo faced violent winds and heavy rains. Power outages were reported and schoolchildren ordered to stay home.
The storm made landfall on Wednesday afternoon.
Workers at the Fukushima nuclear plant were recalled and cranes, hoses and machinery were removed. Plant operators said the typhoon did not cause any further damage.
Japanese oil refining companies halted shipments but refining continued, said Reuters.
The Associated Press has raw footage from the typhoon: