The typhoon will approach the southwestern half of the country on Friday and will advance towards the centre and northeast of the country over the weekend, according to the Japan Meteorological Agency (JMA).
Hagibis has been classified as a very strong typhoon and is expected to cause torrential rainfall and wind gusts of up to 252 kph as well as waves up to 10 metres high along some parts of the coast, Efe news reported.
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.
Japan's two largest airlines, ANA and JAL, have cancelled almost all domestic flights - around 370 - 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.
The JMA has forecast up to 800 mm of rain in the central Tokai region between Saturday and Sunday and 600 mm in Kanto, which includes the Tokyo Metropolitan Area.
Authorities have warned of the risk of flooding, landslides and accidents due to hurricane winds.
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 )