Officials said, 25 people are missing, as rescue teams continued their search for survivors.
On Monday, three people were newly found in a state of cardiopulmonary arrest in Asakura, Fukuoka Prefecture, and one of them was confirmed dead later, according to the prefectural police.
Heavy rain warnings are still in place for parts of the southern island of Kyushu today after Typhoon Nanmadol swept across Japan earlier this week, dumping torrential rain that has wrecked homes, roads and rice terraces.
The deadly disaster prompted Prime Minister Shinzo Abe to decide to cut short his European tour and return to Japan.
A village in Fukuoka Prefecture, Toho, where more than 40 houses were destroyed, said Monday it will construct temporary housing for people affected by the disaster.
"My parents are still trapped with 16 other people in the Kurogawa area and I have absolutely no information about the situation there", Asakura resident Kayoko Ishibashi told AFP on Friday, referring to a district in the city. They suspect the victims were carried downstream by the Chikugo River, which flows through the disaster area.
Fallen trees smashed into houses in the hard-hit Fukuoka prefecture city of Asakura, which saw more than 50 centimetres (almost 20 inches) of rain in a 12-hour period to Wednesday night.
Koki Tokunaga, an 11-year-old who attends elementary school in Asakura, said, "I feel exhausted because I was cleaning up the mud from the road in front of my house with my family".
In a junior high school in Asakura, around 160 students gathered for a ceremony to mark the end of the term and shared a moment of silence.
A public official in his 30s said he took a day off from work in Hiroshima Prefecture to help. "It's not just someone else's problem", the Oita native said.