On Izu Oshima island, located about 120 km south of Tokyo, 13 people were confirmed dead as around 30 houses were completely destroyed by mudslides triggered by the storm.
Record rainfall of 122.5 mm per hour was registered on the island and the Metropolitan Police Department plans to dispatch a special rescue team to the island, said Japan's Kyodo News, adding the Tokyo Fire Department's hyper rescue team is being mobilized.
In Tokyo's Machida, a woman died after being swept away by a swollen river, said the report.
Many other people remain unaccounted for in the Kanto region in the centre of Japan's capital Tokyo, including two boys who were reportedly carried away by high waves in Ninomiya, Kanagawa prefecture, Kyodo quoted the National Police Agency as saying.
The storm also led to suspension of local transportation as several Bullet Train services on the Tohoku, Yamagata, Joetsu, Nagano and Tokaido Shinkansen lines were cancelled, while 193 domestic flights of Japan Airlines and 211 domestic and international flights of All Nippon Airways were scrapped.
Powerful typhoon Wipha hit the central and northeastern parts of Japan.
The Japanese government has set up a liaison office at the prime minister's office to gather typhoon-related information.
As of 11 a.m., Wipha, the 26th typhoon of the year, was moving north-northeast at a speed of around 75 km per hour, some 150 km east-southeast of Ishinomaki in Miyagi prefecture, according to the Japan Meteorological Agency (JMA).
The typhoon is expected to be downgraded to an extra-tropical cyclone Wednesday afternoon in the Pacific Ocean east of the Tohoku region, said the JMA.