Heavy rains fuelled worries of more landslides and with hundreds of aftershocks and fears of more quakes, thousands spent the night in evacuation centres.
"It's full in there. There's not a inch to sleep or even walk about in there. It's impossible in there," a resident of Mashiki town said outside an evacuation centre.
Another survivor said the cleanup would be extensive.
"I can't even imagine when we can start the recovery process. My home is a mess, I don't know what to do next. And all these people affected."
Firefighters handed out tarpaulins to residents so they could cover damaged roofs, but many homes were simply deserted.
About 422,000 households were without water and 100,000 without electricity, the government said. NHK said around 240,000 people had received evacuation orders across the affected region amid fears of landslides.
Troops set up tents for evacuees and water trucks were being sent to the area while television footage showed people stranded after the fall of a bridge being rescued by helicopters.