At least six people died and a university student was missing on Wednesday as record-breaking rains battered parts of southwestern Japan still reeling from earthquakes two months ago, setting off flooding and landslides.

Hundreds of thousands people were advised to evacuate a wide swathe of Kyushu, Japan's southernmost main island, where 49 people died in earthquakes in April that weakened the ground and left it prone to landslides, NHK national news channel reported.

"I was in such a hurry to leave I don't have anything more than what I'm wearing," one elderly woman told NHK at an evacuation center.

Among those killed were a couple in their 80s whose house in Kumamoto was engulfed by mud after some places were hit by more than 100 mm (4 inches) of rain in an hour.

Prime Minister Shinzo Abe was in Kumamoto on Wednesday to kick off campaigning for an election next month for parliament's upper house.

Authorities warned of further landslides in areas where the ground was weakened by a 7.3 magnitude earthquake in April and several thousand people are still living in evacuation centers.

The area has been shaken by a steady series of aftershocks, including one on Wednesday morning.