Government spokesman Yoshihide Suga said the death toll from the disaster reached 201.
With the toll mounting, Prime Minister Shinzo Abe cancelled a four-country foreign trip, and he was expected to visit the disaster-hit region later this week.
The rains are the deadliest weather-related disaster in over three decades in Japan, and the size of the death toll has raised questions about whether authorities were sufficiently prepared. Rescuers are digging through mud and rubble for survivors.
Abe was set to visit Tusk on Wednesday to sign a free trade pact with the European Union but was forced to abandon a trip to Europe to oversee the emergency response to deadly heavy rains.
According to the Japan Meteorological Agency (JMA), an active seasonal rain front caused torrential rain in most eastern and western regions of Japan since last Thursday. More than 70,000 rescuers are looking for dozens of missing people, and thousands remain in shelters.
"We are working hard to rescue them as quickly as possible". "It hurts that our memories are gone". "The disaster happened so suddenly, I am struggling to come to terms with it", the school's principal said.
"Rescuers had to go by boat yesterday due to flooding but water is gradually receding today".
Floodwaters have subsided in most places but left behind massive debris including broken trees, furniture and mangled cars that still need to be moved out of the way.
Prince Louis' Christening -- See All the Royal Pics!
The duchess wore a Ralph Lauren dress , a Stephen Jones hat, Manolo Blahnik shoes, as well as gloves and a clutch. The duchess, who was wearing Alexander McQueen , added, with a smile: "I hope he stays like this".
The rain finally lifted on Monday.
Landslide warnings were issued in more than a quarter of Japan's prefectures. Convenience stores are open shorter hours, and dozens of outlets of major chains such as Family Mart, 7-Eleven and Lawson were closed due to delayed deliveries, supply shortages or flooding in Hiroshima, Okayama and Ehime.
An official there said Wednesday that the alert had been downgraded, but urged residents to remain cautious.
"We want to demonstrate what we have been training for as a center for summarizing and resolving problems such as food poisoning at evacuation centers, and secondary harm accompanying prolonged evacuation", said Yoko So, a doctor who leads the team of experts in public health.
A local resident walks in a flooded area in Mabi town in Kurashiki, Okayama Prefecture, Japan, July 9, 2018.
Authorities said high temperatures were forecast for Monday, posing new challenges for the many people stuck in modestly equipped shelters with few possessions or damaged homes with no water or electricity.
Around 23,000 people are now in evacuation centers after fleeing the historic deluge and 73,000 disaster response workers have been recruited to assist in rescue efforts. "We are keeping up our search-and-rescue work", said Mutsunari Imawaka, an official with Okayama prefecture, adding that over 1,000 people were involved in the effort in the one part of Kurashiki alone. "We were hoping to find two people but still can't find one".