Some 11,200 households had no electricity, power companies said on Monday, while hundreds of thousands had no water. "We are carrying out rescue operations around the clock", Yoshihide Fujitani, a disaster management official in the prefecture, told AFP.
In the town of Uwajima in Ehime Prefecture, a 63-year-old man was buried alive in his house due to landslides.
Some residents in Hiroshima prefecture said they were caught off guard in a region not used to torrents of rainfall, which began Friday and worsened through the weekend.
Even as the rains let up, authorities warned the downpours had loosened earth on hillsides and mountain slopes creating new risks. "There are still many people missing and others in need of help, we are working against time", Prime Minister Shinzo Abe said.
Torrential rains have pounded western parts of the country with three times the usual precipitation for this time of the year, setting off landslides and causing rivers to breach their banks.
Heavy rain was forecast to continue through Sunday in the west and the east, agency official Minako Sakurai told reporters. Some 40 helicopters were out on rescue missions. "This is a situation of extreme danger". While evacuation notices are no longer in effect, two million people are still being advised to keep away from their homes. "There are still many people who have been unaccounted for".
Rescue workers acknowledged the odds of finding people alive were getting longer.
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The operation began at 10 a.m. local time and went faster than initially expected, but did not confirm which boys were rescued. Narongsak said the healthiest have been taken out first, and the next phase of the operation would start in 10-20 hours.
Pope Francis is praying for the victims of Japan's flooding and is encouraging civil authorities involved in search and rescue operations.
The government said at least 103 people had been killed, and with many people still missing, the tally was expected to rise further. Critical infrastructure has been hit, including railway tracks.
Health, Labor and Welfare Minister Katsunobu Kato said at a press conference after a Cabinet meeting on Tuesday that the government would start dispatching the Disaster Health Emergency Assistance Team (DHEAT) from Thursday at the request of the Okayama prefectural government to support hygiene control at evacuation centers.
At least 126 people are now known to have died in floods and landslides triggered by torrential rain in western Japan, says the government.
Israel-based worldwide aid group iAid said it was looking for support to send a team to Japan to help provide clean water and electricity.
President Cyril Ramaphosa sent a message of condolences to the people of Japan on Sunday and said that the thoughts of the South African people are with the people of Japan during this hard time. The Japan Meteorological Agency has reported that one area of the Kochi prefecture experienced a staggering 26.3 centimeters (10.4 inches) of precipitation in just three hours, almost as much as the average amount for the entire month of July (32.8 centimeters or 12.9 inches), typically southwestern Japan's second wettest month after June.