More heavy rain is forecast after Saturday's deadly deluge in the Kumamoto prefecture, Japan's worst natural disaster since Typhoon Hagibis in October last year left about 90 people dead.

Prime Minister Shinzo Abe told a meeting of Japan's disaster response task force to step up the search and rescue operations.

"Nothing is more important than human lives. Please make utmost effort through the night to search for missing people," Abe said after Japanese television broadcast images of overturned cars, people shoveling mud from their homes and the military rescuing stranded residents in boats.

"We had no electricity and no running water," one rescued woman told the broadcaster. "It was tough."

TV footage also showed a gymnasium-turned-evacuation center equipped with face masks, disinfectants and thermometers to prevent coronavirus infections.

The Japan Meteorological Agency urged people to stay vigilant, as more rains are predicted.

"From this evening on, extremely heavy rains with thunder are expected in southern as well as northern Kyushu," an agency official told Reuters.

"The rainfall so far has already loosened the ground. There is a high chance of landslides occurring, even without much additional rain."