Thousands of households have lost power and Japan’s two largest airlines have suspended many flights.
The adverse weather has also forced the suspension of a search operation for missing people after a volcanic eruption in central Japan last week.
Japan averages 11 typhoons a year, according to its weather agency.
Typhoon Phanfone was downgraded from an earlier status of a super typhoon, but the Japan Meteorological Agency warned that it was still a dangerous storm with winds gusting to 135mph.
The typhoon is moving at a speed of 12.5 mph from off Japan’s south-western coast and is expected to make landfall and approach the capital Tokyo on Monday, October 6.
The storm is expected to deposit about 100mm of rain on Tokyo over 24 hours, according to the Transport Ministry website.
Many schools will close on October 6 and two car companies in Japan have halted production at some plants ahead of the storm.
More than 174 domestic flights were affected nationwide, NHK state broadcaster said on Sunday, October 5.
Twelve people are still missing following the eruption of Mount Ontake in central Japan.
The volcano, about 125 miles west of Tokyo, erupted last Saturday killing 51 people, mostly hikers. It is still emitting poisonous fumes.
Heavy rain delayed the Japanese Formula One Grand Prix on Sunday, and French driver Jules Bianchi was rushed to hospital after losing control and crashing in the wet conditions.
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