The deluge follows a period of punishing heat in many parts of Japan, with a national record temperature of 41.8C set this week.

Television footage showed brown, fast-flowing water overflowing its banks to inundate homes in the Kagoshima region.

Local media reported that Kirishima city, Kagoshima, saw a record rain of 500 millimetres in the 24 hours through 5:00 am, twice the average rainfall for the entire month of August.

The Japan Meteorological Agency (JMA) said the region was "seeing heavy rains that it has never experienced before," but it downgraded its highest alert for heavy rain as the downpour eased.

"Even though the warning has been downgraded, please remain vigilant and ensure your safety," JMA official Shuichi Tachihara said at a press conference.

"Even a small amount of rain could increase the risk of disaster. Please continue to be on high alert for landslides and river flooding," he said.

Over 122,000 residents in Kirishima were urged to evacuate, while the warning was lifted for people in the neighbouring Miyazaki region.

More than half a million people had earlier been encouraged to leave their homes.

Two people were rescued from a collapsed house after a landslide in Aira, another city in Kagoshima, a local fire department official told AFP.

A woman in her 30s, also believed to be a resident of the house, is missing.

Domestic flights at Kagoshima airport were cancelled.