Rescuers were hard at work searching for dozens still missing in south-western Japan on Monday after heavy rain caused flooding and mudslides.

Residents returning to their homes were left speechless and unsure where to start the recovery and clean-up due to the extent of the damage.

At least 100 people died or are presumed dead, with more than 60 still unaccounted for, most of them in the hardest-hit Hiroshima area.

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Rescuers search for missing people in Kumano town, Hiroshima prefecture (Sadayuki Goto/Kyodo News/AP)

Seiji Toda was shocked and helpless when he saw his restaurant, which he opened nearly 40 years ago, filled with mud heaped about a yard (1m) from the floor. Tables, covered with clean white tablecloths before he left, were all mud-covered, chairs thrown to the floor.

“I had never seen anything like this,” he said on TBS television, standing outside his restaurant in Hiroshima city while wearing a helmet. He said it would be impossible to clean up the mess by hand.

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A man cleans debris caused by heavy rain in Soja, Okayama prefectur (Kyodo News/AP)

Right next to his restaurant were heaps of broken trees and other debris. Several cars were still half buried in the mud.

The assessment of casualties has been difficult because of the widespread area affected by the rainfall, flooding and landslides since late last week.

Authorities warned that landslides could strike even after rain subsides as the calamity shaped up to be potentially the worst in decades.

Some homes were smashed. Others were tilting precariously. Rivers overflowed, turning towns into lakes, leaving dozens of people stranded on rooftops. Military paddle boats and helicopters have taken people to safety.

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Rescuers prepare to start a search for missing people at the site of a landslide in Kumano town, Hiroshima prefecture (Sadayuki Goto/Kyodo News/AP)

Chief Cabinet Secretary Yoshihide Suga said on Monday that 87 people were confirmed dead and 13 others were without vital signs when they were found.

Prime Minsiter Shinzo Abe said the government has expended the search and rescue effort, dispatching 73,000 troops and emergency workers.

“The rescue teams are doing their utmost,” he said.

In large parts of Hiroshima, water streamed through a residential area, strewn with fallen telephone poles, uprooted trees and mud over the weekend.

Restaurant owner Mr Toda said he took precautions because of his fresh memory of flooding four years ago that killed more than 70 in Hiroshima. Others were caught off guard.

“It gives me a chill thinking what could have happened,” said Eiko Yamane on Sunday as she recalled realising how suddenly water was reaching the tyres of the car she was driving. She was able to escape.

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Emergency rescue teams recover the body of a flood victim in Hiroshima, (Haruka Nuga/AP)

The Japan Meteorological Agency said three hours of rainfall in one area in Kochi prefecture reached an accumulated 10.4in (26.3cm), the highest since such records started in 1976.

A couple were found dead in a farmhouse buried in a mudslide in Kagoshima prefecture on Monday.

Earlier, a woman who was reported as missing after getting trapped in her car was found dead, Kyodo news service reported.

Kochi prefecture, on Shikoku, issued landslide warnings over almost the entire island.

The Japanese government set up an emergency taskforce over the weekend and has sent troops, firefighters, police and other disaster relief.

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Elderly people from a nursing home take shelter following heavy rain, in Soja, Okayama prefecture (Takaki Yajima/Kyodo News/AP)

People have also taken to social media to plead for help.

Okayama prefecture, south of Hiroshima, said in a statement that five people had died, seven were missing and 11 were injured, at least one of them seriously.

Nine homes were destroyed and dozens more were damaged, while more than 500 were flooded.