Heavy rainfall caused by a major storm caused landslides and floods in central Japan, killing two people by Thursday morning.
In Nagano prefecture, rainfall elevated by storm caused floods and landslides, and killed a 12-year-old boy, according to Japanese media reports.
Footage showed broken bridges and train tracks as workers began clearing up on Thursday.
Neoguri, which hit Okinawa on Tuesday at typhoon strength, was downgraded to a tropical storm Wednesday after losing strength.
In southern Japan, Kagoshima Prefecture and Miyazaki Prefecture issued evacuation orders overnight.
Miyazaki prefecture said 162 people were evacuated, but the orders were lifted by Thursday morning, while Kagoshima had orders still in place in parts of the prefecture.
The torrents of rainfall could trigger more landslides and floods, and much of eastern Japan was at risk of lightning and tornadoes.