Landslide warnings were issued in more than a quarter of the nation's prefectures.
The country's west was lashed by heavy storms last week and during much of the weekend, bringing flooding and landslides which led to Japan's worst natural disaster since the 2011 tsunami and quake that prompted the Fukushima nuclear accident.
As the floods receded, emergency workers reached previously cut-off places where authorities fear they could find more bodies in the wreckage of homes devastated by rivers of mud and debris.
In Kurashiki, the receding floods have left a layer of silt on everything that was underwater.
"The thoughts of the South African people are with the people of Japan during this hard time‚" Ramaphosa said.
Over 75,000 police, firemen and troops have been deployed to dig through the rubble looking for survivors, or victims of the disaster. Two billion yen ($18 million) had been pledged to deliver emergency food, water, and relief essentials such as toiletries, air conditioners, and temporary bathing facilities.
Yoshihide Suga, Japanese government spokesman, said the whereabouts of 92 people were unknown, mostly in the southern area of Hiroshima prefecture.
In neighbouring Okayama prefecture, rescue workers flew in helicopters over areas that are still submerged and otherwise unreachable, looking for signs of life.
Across nine other prefectures including Osaka, Yamaguchi and Tokushima, the ministry said that 1,100 homes remain without water supply and the likelihood of it being restored is extremely minimal.
The record rainfall since July 5 in the Japanese archipelago led to severe floods and landslides, particularly in Hiroshima, Ehime and Okayama prefectures where the disaster has ravaged thousands of homes and cut off access to several neighbourhoods.
The Internal Affairs and Communications Ministry's Fire and Disaster Management Agency announced that 23,369 people stayed in shelters as of Sunday night.
While persistent rain had ended, officials warned of sudden showers and thunderstorms as well as more landslides on steep mountainsides saturated over the weekend. "I've never seen this before", the 69-year-old oyster farmer told AFP.
In the town of Motoyama, about 600km (370 miles) west of the capital Tokyo, 583mm (23in) of rain fell between Friday morning and Saturday morning, Japan's meteorological agency said. "I've been living this town for nearly 70 years, but it was first time to have such heavy rain".
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The government has reportedly struggled to offer exact information about the number of children separated from their parents. Handout/Reuters Baby and toddler high chairs are seen at the Bristow facility, in this photo provided by the U.S.
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