Warnings for heavy rain and flooding were issued in large parts western and southern Japan.
At least 50 people are dead and about 50 missing due to torrential rains which continued to fall on Saturday across a wide area of western Japan, causing landslides and flooding that destroyed homes and swept away cars.
People wait to be rescued on the roof of a house nearly submerged in floodwaters caused by heavy rains in Kurashiki, Okayama prefecture, southwestern Japan on Saturday.
The downpour, which began Thursday, is likely to last till Sunday.
Record-breaking torrential rains struck western Japan, causing at least 44 deaths and leaving dozens injured.
Of those killed, nine were confirmed dead in Hiroshima, local authorities said, with the rest dying in Osaka, Shiga, Hyogo, Okayama and Ehime prefectures. Some parts of Japan were set to see up to 400 mm of rain in the coming 24 hours, with the rain set to continue until Sunday.
The country's Fire and Disaster Management Agency said more than 150,000 residents were ordered to evacuate, and another 1.2 million were urged to flee Friday morning as conditions worsened, Reuters added.
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As the rescue operations continued, the country also saw a 6.0-magnitude quake just outside Tokyo on Saturday, which left buildings swaying in the capital.
In the prefectural capital of Hiroshima, a vehicle with a mother with her three children was swept away by flood waters in the city's Aki Ward. One person in the building died and another remains unaccounted for while four others are conscious. Landslides occurred in several locations in Hiroshima Prefecture on the night of July 6, and there are reports that residents were buried.
But the orders are not mandatory, and many people have become trapped inside homes that were engulfed by floodwaters or hit by landslides. On Nuwa Island, off the prefectural capital of Matsuyama, a woman in her 30s and her two children were killed when a mudslide hit their home. On Saturday, rescue workers transferred them to safety, by carrying them through swiftly flowing dark waters.
In some areas of the island, the storms brought as much as twice the average July rainfall for the entire month, Reuters also said.
Mitsubishi Motors Corp halted operations at one plant because it could not get parts, Kyodo said.
Japan's Prime Minister Shinzo Abe told his ministers to "make an all-out effort" to rescue victims, saying: "The situation is extremely serious".