Mindulle, the ninth typhoon this season in the Pacific and classified as "strong", lashed the Japanese capital and its suburbs with winds of up to 180 kmph and caused heavy rainfall and landslides that paralysed key air and rail networks, Efe news reported.
The typhoon has left behind waterlogged streets and travellers trapped at airports and train stations owing to cancellations.
The storm made landfall around midday in the south of Chiba prefecture, to the east of Tokyo, where it left some 84,900 homes without electricity and 15 persons injured.
Injuries were also reported from the prefectures of Kanagawa, Tokyo, Shizuoka, Gunma and Ibaraki.
More than 500 domestic and international flights to and from Tokyo's Haneda and Narita airports were cancelled and operations of over 100 trains in the region were suspended.
The Japan Meteorological Agency (JMA) has advised people to stay indoors and warned against going near the coast or river banks due to strong waves and overflows.
The JMA has also issued a red alert for heavy downpour in 14 prefectures in eastern, central and northeastern Japan, including Tokyo, Kanagawa, Saitama and Chiba, which are among the most populated in the country.
At 6.50 p.m. Mindulle was moving northwards at 35kmph towards northeast of Honshu island, after which it is expected to reach Hokkaido.
On Sunday, Hokkaido faced the brunt of typhoon Kompasu, the eleventh of the season, which left one person dead -- a man found on Monday inside his inundated car -- according to NHK broadcaster.
