Record rainfall has caused flooding and landslides in which 26 people have been killed and hundreds of thousands affected.
Many are staying in evacuation centres as rescue teams searching for those missing.
Troops and police are concentrating their rescue operation on the northwest of Kyushu, where some 5000 people are stranded after roads were swept away.
Japan's Self-Defence Forces have been brought in to help search for a number of people still missing.
Heavy rain has also caused flooding in Japan's historic capital, Kyoto, and 250,000 people have been ordered to leave their homes in the prefectures of Fukuoka, Saga, Kumamoto and Oita.
In Fukuoka prefecture alone, about 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, local officials said.
