Japanese police search for missing people buried under mud at the scene of a landslide following days of heavy rain in Atami in Shizuoka Prefecture, Japan on Monday. Photo: AFP

Japan braced for further downpours on Sunday as rescuers sifted through flood and landslide damage after record rain that left at least three dead.

Residents returned to check on their mud-covered homes in the southwest, where nearly 2 million people were advised to urgently seek shelter Saturday as rivers overflowed.

"So many logs tumbled down and crashed into this area" from nearby mountains, an elderly resident of Kanzaki in Saga Prefecture told public broadcaster NHK.

"It was so, so scary," she said. "You absolutely have to leave when it rains."

More than a meter of rain has been recorded since Wednesday in the northern part of Kyushu, one of the places hardest hit by a band of intense wet weather stretching across Japan.

Showers had eased in the region on Sunday, with the weather agency downgrading alerts from the top level, but more rain was expected from the evening.

"We have not started to survey human or property damage on a full scale," said Hironori Fujiki, a city official in Kyushu's Nagasaki Prefecture.

Two women in their 70s were confirmed dead after they were found in a drainage canal, Fujiki said.

It came after a 59-year-old woman died in a landslide that swept away her house in Unzen, Nagasaki, on Friday.

Rescue workers are still combing the wreckage for two of her family members.

Landslides were also seen in other parts of Japan, with three people including a child under 10 feared dead after a family home was engulfed in central Nagano region, a local official told AFP on Sunday.

Scientists say climate change is intensifying the risk of heavy rain in Japan and elsewhere, because a warmer atmosphere holds more water.

AFP