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

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.

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.

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.

Domestic flights at Kagoshima airport were cancelled because of the rain.