At least 50 people have died and a dozen are missing.

Pounding rain since late Friday in Japan's southern region of Kyushu has triggered widespread flooding. More rain was predicted in Kyushu and the western half of Japan's main island as the rain front moved east.

In Fukuoka, on the northern part of the island, three soldiers waded through knee-high water pulling a boat carrying a mother, her baby and two other residents.

"Good job!" one of the soldiers said as he held up the baby to his chest while the mother got off the boat, Asahi video footage showed. Several children wearing orange life vests over their wet T-shirts arrived on another boat.

The Fire and Disaster Management Agency said 49 victims were from riverside towns in the Kumamoto prefecture. Another of the dead confirmed as of Tuesday morning was a woman in her 80s found in her flooded home in another prefecture.

About three million residents were advised to evacuate across Kyushu, Japan's third-largest island.

Tens of thousands of army troops, police and other rescue workers mobilised from around the country worked their way through mud and debris in the hardest-hit riverside towns along the Kuma River.

Rescue operations have been hampered by the floods and continuing harsh weather.

In Kuma village in the hardest-hit Kumamoto prefecture, dozens of residents took shelter at a park. The roofed structure had no walls or floor and they sat on blue tarps spread on the dirt ground, with no partitions. The village office's electricity and communications had been cut.

Among the victims were 14 residents of a nursing home next to the Kuma River, known as the "raging river" because it is joined by another river just upstream and is prone to flooding. Its embankment fell, letting water gush into the nursing home.

Australian Associated Press