The government said at least 100 people had been killed, and with many people still missing, the tally was expected to rise further.
Public broadcaster NHK said flooding and landslides were hindering rescue efforts and repeatedly urged people not to lose hope.
Japan's National Police Agency has sent additional patrol units to western parts of Japan to protect property left empty by flooding.
Many people are still believed to be stranded inside their homes due to them not having access to roads, access roads being flooded or general flooding, local media reported Monday.
Search and rescue operations have been continuing in disaster-hit areas, like Hiroshima Prefecture where 44 people have been pronounced dead.
Transportation services have been severely disrupted since Thursday, with Shinkansen bullet train services partially suspended in most parts of western Japan and major arterial highways partially closed.
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At one point, officials issued evacuation orders for almost 6 million people in 19 prefectures, Kyoda News reported. About 40 helicopters were out on rescue missions.
A convenience store worker, who had fled to a nearby rooftop, said water had reached as high as his head.
Television footage showed bridges and cars washed away by raging rivers and flood waters, with people perched on the roofs of their homes, surrounded by water and awaiting rescue.
Most of the deaths occurred in the Hiroshima prefecture, where hundreds of homes were damaged.
"We've never experienced this kind of rain before", an official at the Japanese Meteorological Agency (JMA) told a news conference.
In Uwajima town in Ehime prefecture, an overflowing river washed debris down to the coast, turning seawater partially muddy.
These businesses include automakers Toyota Motor Corp., Mazda Motor Corp. and Daihatsu Motor Co.
Japan monitors weather conditions and issues warnings early, but its dense population means every bit of usable land is built on in the mostly mountainous country, leaving it prone to disasters.