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 Kagoshima.

Around 530,000 people in the prefecture, as well as in neighbouring Miyazaki, were urged to evacuate or take alternative measures, the fire and disaster management agency said.

Kagoshima "is seeing heavy rains that it has never experienced before", an official of the Japan Meteorological Agency (JMA) told a press conference.

"Lives are at risk... We ask that you secure your safety by moving to buildings located even slightly away from streams or cliffs, or to buildings less prone to flooding," he said, noting that dangerous conditions may already exist in affected areas.

The JMA official also urged residents to evacuate without waiting for orders from municipalities.

A land ministry official warned in the same press conference about the risks of rivers bursting their banks.

Kirishima, a city in Kagoshima, told residents to evacuate or take alternative measures following the JMA's special warning -- the highest on its five-scale system.

"Rivers are swelling, posing a risk of flooding, or flooding may have already occurred over the levees," the city said on its website.

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.

There were reports that several other houses had collapsed in the area, public broadcaster NHK reported, citing unnamed local officials, while top government spokesman Yoshimasa Hayashi said there had been many reports of flooding.

More than 490 millimetres (19 inches) of rain fell over 24 hours through 4:40 am (1940 GMT Thursday) in one area of Kagoshima -- its largest recorded downpour, according to Kyodo News.

Domestic flights at Kagoshima airport were cancelled.