Torrential rain that began late last week left one person missing and four others injured in the southern prefecture of Kagoshima.
A low-pressure system stuck over the region has since dumped more rain in the northern parts of Kyushu.
The Japan Meteorological Agency issued the highest-level warning in Kumamoto. The Fire and Disaster Management Agency issued evacuation advisories to tens of thousands of people in Kumamoto and six other prefectures in the region.
Rescue workers were searching for several people.
In Kumamoto, they were looking for three people. A family of three was hit by a mudslide while driving to an evacuation centre; two were dug out alive but a third person was still missing. Two others were missing elsewhere in the prefecture.
Several other people were also reported missing after falling into swollen rivers in Kumamoto and nearby Fukuoka prefecture.
Television footage showed muddy water gushing down, carrying broken trees and branches, and residents wading through knee-deep floodwater.
Prime Minister Shigeru Ishiba said his government was supporting search and rescue operations for the missing and helping others in affected areas.
He urged residents "to use maximum caution", encouraging them to "please prioritise actions to save your lives".
Heavy rain also impacted people travelling during Japan's Buddhist "bon" holiday week.
Bullet trains connecting Kagoshima and Hakata in northern Kyushu, as well as local train services, were suspended.
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