At least 17 people died, 20 were missing and 50,000 were ordered to evacuate as the heaviest rainfall on record pounded the southwestern Japanese island of Kyushu, officials and reports said Thursday.

Emergency workers in Kumamoto prefecture responded to multiple reports of mudslides swallowing houses and people being trapped, with access roads blocked by mud or gushing water, officials said.

Troops have been deployed with nearly 100 millimetres (four inches) of rain falling in an hour in some areas.

"Particularly in Kumamoto and Oita prefectures, we are seeing the heaviest rain that (the region) has ever experienced," the Japan Meteorological Agency said.

Kyodo news agency put the death toll at 17.

Kumamoto prefecture confirmed the deaths of five women in their 60s, 70s and 80s and an 87-year-old man after waters destroyed their houses.

The local government has received reports of at least 19 missing people, many of them swept away by swollen rivers or going missing after their homes were destroyed.

"Unfortunately, we believe the numbers (of dead and missing) will rise as we get more and more information from the field," a Kumamoto spokesman told AFP.

Local emergency responders have received "many requests" for rescue operations, the spokesman added.

"We may get more rain later and we are increasing our alert level for rivers overflowing," another Kumamoto official said.

In neighbouring Oita prefecture, a man in his 70s died after being swept into a raging river, while another man remained missing.

Prime Minister Yoshihiko Noda promised full relief efforts to help affected residents.

"I have heard that this is a record for heavy rainfall. We will take effective measures," he said in a legislative session.

Self Defense Force troops have been deployed to the region for disaster relief efforts at the request of local governors.

The prime minister's office in Tokyo has established a liaison office to coordinate efforts among central government ministries to deal with the disaster.

In Kumamoto prefecture more than 17,000 households had been ordered to evacuate, with 5,000 more advised to seek shelter elsewhere.

Oita authorities issued evacuation orders to nearly 15,000 people and advised a further 10,000 to leave.

In all, more than 50,000 people in Oita and Kumamoto received evacuation orders, according to local media.