The weather had eased somewhat by Friday morning, but the Japan Meteorological Agency said it expected "very heavy rain" again in Kyushu later on Friday.
The downpours were set to add to the misery for an area where 50,000 people were ordered to leave their homes on Thursday after it was lashed by the heaviest rainfall on record.
"We expect heavy rain on the same scale we saw yesterday will fall again today. We remain on the highest alert," said a local official in badly-hit Oita prefecture.
An official in Kumamoto prefecture, neighbouring Oita, said at least 18 people were known to have died, with troops and rescuers continuing their search for seven still missing.
In Oita, a man in his 70s died after being swept into a raging river, while another man remained missing.
The weather agency urged residents of Kyushu to continue exercising vigilance against mudslides and floods after rainfall of 10.1 centimetres (about 4 inches) per hour was recorded in the southern region of Kagoshima early Friday.
-AAP