The storm is already battering Chiba prefecture where violent gusts have torn roofs off homes and left some residents with injuries, reports public broadcaster NHK.
The Japan Meteorological Agency (JMA) officials have classified typhoon Hagibis as "very strong".
The storm is moving northwards over the Pacific towards Honshu.
Hagibis could be on par with a typhoon that killed more than 1,200 people in the Kanto and Izu regions in 1958.
The agency has issued an emergency warning for landslides in Tokyo and Izu, Shizuoka prefecture.
It's forecasting torrential rain through Saturday with a severe risk of floods and landslides.
The Japanese government has convened an emergency meeting to take preventive measures and has asked citizens in central, south and west Japan to remain vigilant over the weekend, Efe news reported.
Japan's two largest airlines, ANA and JAL, have cancelled almost all domestic flights scheduled to or from the two Tokyo airports (Haneda and Narita) and some of the connections between Osaka and Chubu.
Shinkansen bullet train services between Tokyo and Nagoya have also been suspended, the Central Japan Railway Company announced on Friday.
Hagibis has also led to the cancellation of two Rugby World Cup games scheduled for Saturday and could also affect this weekend's Grand Prix at Suzuka.
( With inputs from IANS )