A storm has dumped 500 millimetres of rain in just eight hours in southern Japan, killing several people and forcing thousands to evacuate their homes.

The rain pounded the island of Kyushu in Japan's south-west, with some parts of Kumamoto prefecture copping the full brunt of the deluge.

In the city of Aso, an 80-year-old woman was killed after being washed away, and officials say two other people have been confirmed dead in the city.

Two women were killed after floodwaters destroyed their homes in the village of Minamiaso.

At least five people are believed to be missing, and emergency workers say there are multiple reports of mudslides swallowing homes.

In the city of Kikuchi, a home was swept way with a man and a woman still inside. They were later rescued.

Fearing more landslides, officials have ordered 50,000 people to evacuate their houses.

The heavy rains have also caused blackouts and wreaked havoc on railway services and motor traffic.

Prime minister Yoshihiko Noda says he has received a report on the unprecedented rainfall and will take sufficient anti-disaster measures.

The government has set up a liaison office within the crisis management centre at the prime minister's office.

ABC/Kyodo