At 11.40 a.m., Malakas, categorised as "strong" by the Japan Meteorological Agency (JMA), was off the west coast of Tokushima prefecture where more than 4,660 people were evacuated, EFE news reported.
The evacuation of 20,400 people has been recommended in several regions of Kobe city which faces the danger of landslides.
Malakas, the 16th typhoon of the season in the Pacific, made landfall in Kagoshima prefecture after midnight where in some areas more than 100 mm of rain per hour was recorded.
The typhoon led to the cancellation of at least 101 domestic flights at Tokyo's Haneda Airport.
Heavy rains have caused the river in Nobeoka town to overflow leaving several areas inundated.
Malakas was moving northeast at a speed of 35 kph with wind gusts of up to 180 kph, according to JMA.
JMA expects that the typhoon will continue moving from the western coast to the east during the day until it turns into a tropical storm on Wednesday.
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