Authorities lifted "special" heavy rain warnings for the hardest hit prefectures of Fukuoka and Oita, although lesser warnings remained in place.
At least 11 people were missing or could not be reached, including a child, and many more were stranded and calling for help across areas of Fukuoka and Oita prefectures on the Japanese island of Kyushu.
As of 2:10 p.m. on July 6, the JMA had issued heavy rain warnings covering all of Oita Prefecture, with landslide warnings in the cities of Nakatsu, Hita, and Taketa, and the town of Kokonoe.
Those included a child reportedly carried off by a fast-flowing river and a couple who had not been seen since their house was swept away.
Another man, a 93-year-old, was likely swept away by flooding. His body was found on Wednesday washed up in Asakita in Hiroshima prefecture. "Seven of us are trapped on the second floor of a factory".
Officials said the military presence could be expanded up to 5,000 people and 50 helicopters if needed.
"I heard smashing and banging in the house, windows shattering, then floodwater gushed into the house, furniture floating around", said Tsunemichi Motomatsu, who runs a liquor store with his wife.
About 400,000 people have been ordered to leave their homes, mainly in Fukuoka and Oita prefectures.
Japan Meteorological Agency warned of flooding, mudslides and swollen rivers in some areas of western Japan.
It said 1,800 people had sought refuge in schools and other public facilities in Fukuoka as of early Thursday.
The government's top spokesperson added that 7,800 police officers, firefighters and Self-Defense Forces (SDF) personnel had been dispatched for search and rescue operations and are working closely with prefectural and municipal officials in the affected areas. "We will keep in close contact with the disaster-hit areas and work with all our energy to save lives and ascertain the extent of the damage".