Typhoon Wipha, dubbed the strongest in a decade, caused landslides that buried houses as it churned past an island just south of Tokyo.
Public broadcaster NHK and Jiji Press reported at least 16 people had died and 51 were unaccounted for on Oshima, after houses were destroyed or swept away by a series of landslides and floods on the island, 120 kilometres south of the Japanese capital.
"We've confirmed that 13 people have died, and the number is likely to increase later," a police official in Oshima earlier told AFP.
Many of the bodies of those who died on Oshima were found in houses that had been splintered by huge volumes of earth sent crashing down mountainsides by torrential rains and strong winds.
Footage from the island showed ruined wooden houses half buried in mud. Mangled trees and other debris were piled up around them.
The storm dumped more than 12 centimetres of rain on Oshima in an hour, according to the meteorological agency.
Many local residents had sought shelter in evacuation centres, reporting dirty water had been gushing into their homes, according to local media.
The bodies of two of those who died were discovered in a swollen river, while one other was pulled from a crushed house, NHK said.
"City hall and fire station officials are doing rescue work in places accessible," a local official told AFP.
The local authority has not been able to confirm the whereabouts of 51 of the island's more than 8,300 residents, Jiji Press reported.
It was not known if they were simply unable to make contact or if their situation was more grave.
Japanese troops have also sent three helicopters and several servicemen to Oshima to help with the rescue effort at the request of the Tokyo Metropolitan government, a defence ministry spokesman said.
In western Tokyo, a woman who appeared to be in her 40s was confirmed dead at a hospital after she was discovered in a river, making the total death toll to 17, police and reports said.
A further three people were missing in the greater Tokyo area, officials and reports said.
