Flooding and landslides on the southern island of Kyushu have left at least 20 people dead in the past three days.
TV footage showed muddy waters sweeping through homes and streets as rivers burst their banks in the north of the island.
The Japan Meteorological Agency has warned of further rain and landslides.
More than 75cm (30in) of rain fell in 72 hours in the city of Aso, in Kumamoto prefecture, according to weather officials quoted by the French news agency AFP.
The evacuation orders affect 85,000 households in the prefectures of Fukuoka, Saga, Kumamoto and Oita, the Kyodo news agency reported.
In Fukuoka prefecture alone, around 190,000 people from 65,000 households were issued the order, with the entire area of the cities of Yanagawa, Yame and Miyama to be evacuated.
Another 140,000 have been advised to vacate their homes as well, AFP quoted local officials as saying.
Those being asked to leave their homes have been told to go to designated shelters such as schools and other facilities, according to the agency.
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