The death toll from torrential rain and landslides in western and central Japan rose to 88 people early on Monday, with dozens still missing after the rescue of more than 2,000 were temporarily stranded in the city of Kurashiki.
Shinzo Abe, Japan's Prime Minister, has warned of a "race against time" to rescue flood victims as authorities issued new alerts over record rains.
"Rescues, saving lives and evacuations are a race against time," Abe said as he met with a government crisis cell set up to respond to the disaster.
"This is a situation of extreme danger," an official at the Japanese Meteorological Agency (JMA), told a news conference.
Over two million people have been told to evacuate, but the orders are not mandatory and many remained at home, becoming trapped by rapidly rising water or sudden landslides.
The meteorological agency issued its highest level alert for two new regions on Sunday, while lifting the alerts for other areas where rains were subsiding.
Emergency warnings for severe rain in 11 prefectures - the most since a new warning system was introduced in 2013 - had been lifted by evening, but advisories for heavy rain and landslides remained in effect in many areas.
TV footage showed convenience stores with shelves mostly bare while elsewhere, residents lined up to receive water. Some 276,000 households were without water supply.
Roads were closed and train services suspended in parts of western Japan while Shinkansen bullet train services resumed on a limited schedule after being suspended on Friday.
The rain began late last week as the remnants of a typhoon fed into a seasonal rainy front.
Automakers including Mazda Motor Corp and Daihatsu Motor Co suspended operations at several plants on Saturday and were to decide later on Sunday on plans for the coming week.
Electronics maker Panasonic Corp said one plant in Okayama, western Japan, could not be reached due to road closures, although it had been closed for the weekend anyway. A decision about next week would be made on Monday, it said.