A rare emergency warning and evacuation orders for almost 850,000 people were in place as the severe weather struck, standard.co.uk reports.
Dramatic images showed people wading through knee-deep water in flooded streets after several rivers broke their banks on Wednesday.
Highest alert level of five was put in place by Japan's meteorological agency.
The Ground Self Defense Force - Japan's military - said it had deployed about 100 troops for disaster relief after a request from Saga.
Public transportation and businesses were hit, with Toyota Motor Corp saying it would suspend work on Wednesday evening at a factory in Kyushu that builds Lexus cars.
Daihatsu Motor also said it would stop work at factories in the region.