Tens of thousands of rescue workers in Japan have been searching through the wreckage of houses shattered by deadly floods and landslides in a desperate search for survivors amid a rising death toll and looming torrential rain.

Nearly 40 people are feared dead after record rains lashed areas of southwestern Japan in the early hours of Saturday, causing rivers to break banks and flooding low-lying regions.

Although the rain has subsided from its peak levels, the floods washed away roads and bridges, leaving many in isolated communities cut off.

Emergency services, aided by people in rafts, managed to rescue about 50 staff and residents from a nursing home facility, bringing them to safety by boat.

The Japan Meteorological Agency issued a non-compulsory evacuation order for hundreds of thousands of residents in Kumamoto and neighbouring Kagoshima prefectures.

Up to 250mm of rain is expected in the 24-hour period through Tuesday morning in the southern part of Kyushu Island, which includes areas hit hard by the flooding, the agency said.

Japan is currently in the middle of its annual rainy season which frequently delivers deadly floods and landslides.