The Japan Meteorological Agency warned of more landslides and floods on the main southern island of Kyushu as rainfall of up to 11 centimetres (4.3 inches) per hour was recorded early Saturday.
Evacuation orders had been issued to about 240,000 people in the north of Kyushu where more rivers burst their banks, public broadcaster NHK and Jiji Press news agency reported, compiling figures from various authorities.
They were told to go to designated shelters such as schools and other public facilities, while more people were advised to leave their homes.
Television footage showed torrents of muddy, debris-strewn water and flooded houses following what officials described as “unprecedented” downpours from a weather front on Thursday.
Along the Yamakuni river in Oita prefecture, water was seen reaching the roof of a riverside drive-in restaurant.
More than 75 centimetres of rain fell in 72 hours in the inland city of Aso, the meteorological agency said.
The death toll remained at 20 overnight and seven missing, with 19 of the fatalities from landslides and house collapses in and near Aso.