At least 10 people were missing, including a child, and 400,000 were forced from their homes after record rains battered southwestern Japan for a second day on Thursday, sending rivers surging over their banks, a government official and media said.
Parts of Fukuoka prefecture on the southwestern island of Kyushu were hit by 774mm of rain in nine hours on Wednesday, about 2.2 times the amount of rain that falls in a normal July, NHK national television said.
Some 7500 rescuers, including police, firefighters and soldiers from Japan's Self Defence Forces, were mobilized to help with evacuations and search for the missing. Forty helicopters were on standby until the weather improved.
"There are many reports of people whose safety cannot be confirmed, things like 'a child was swept away by the river' and 'my house was swept away and I can't get in touch with my parents'," chief cabinet secretary Yoshihide Suga told an emergency early morning news conference.
"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," he said.
Fukuoka and Oita prefectures, both largely rural areas, were the worst-hit by the rain, which was caused by a low pressure area on the Pacific Ocean that fed warm, moist air into Japan's seasonal rainy front.
Residents spent a worried night at evacuation centres set up at schools and government buildings on high ground amid reports of landslides and flooded roads.
"It wasn't just the rain, there was thunder and lightning too. I couldn't see anything ahead of me," one woman at an evacuation centre told NHK.
A schoolboy sitting with his family told NHK: "I haven't heard from some of my friends, and I'm really worried."
There were no immediate reports of major transportation problems, but television footage showed a railway line left broken and twisted by floodwaters.
The same area was pounded by heavy rain earlier this week from Tropical Storm Nanmadol, which has since passed out to sea.
The rain in Japan comes on the heels of a storm system that caused severe flooding across southern China that killed 56 people and cost almost $4bn in damage.