The nation's Meteorological Agency lifted the emergency warnings in Hiroshima Prefecture on Saturday, while the state of emergency is still in effect in Okayama, Tottori, Hyogo and Kyoto prefectures.
Record downpours prompted authorities to order some 1,932,000 people to evacuate their homes mainly in western Japan, according to the Fire and Disaster Management Agency, but NHK said the figure had risen to almost 3.2 million. Government officials are warning people in affected areas they are at risk for landslides, flooding, wind gusts and other extreme weather conditions.
In Kochi Prefecture in western Japan, more than 900 mm of rain fell over a 48 hour period, leading to prefectural officials to seek the assistance of the Ground Self Defense Force to help with search and rescue operations. As a result, many people died in landslides.
"We are carrying out rescue operations around the clock", Yoshihide Fujitani, a disaster management official in Hiroshima prefecture, told AFP.
The deluge, triggered by the seasonal rain front, brought mudslides and flooding across widespread areas from Shiga Prefecture to the east to Fukuoka Prefecture to the west due to the slow-moving rain front.
Among the missing were five people who got buried when housing collapsed, also in Hiroshima prefecture.
In Hiroshima, a woman in her 40s died in a landslide and a man found in a swollen river was confirmed dead, while another man died after he called a fire station to report that a mudslide had struck his home.
As many as 16 lakh people have been evacuated from their homes, Reuters reported.
Rescuers were searching for 46 missing people on Saturday.
TV footage showed crews in military trucks delivering emergency water supplies to areas where water infrastructure was down, while troops in boats helped people and pets safely reach dry land.
"Water came to the middle of the second floor", a woman in Kurashiki, Okayama wrote, posting a picture of her room half swamped by flooding.
Transportation services have been severely disrupted since Thursday, the transport ministry said, with a number of Shinkansen bullet train services partially disrupted and major arterial highways partially closed.
Two other people were feared dead after being found in buildings hit by landslides, NHK said.
Japanese Prime Minister Shinzo Abe told his cabinet on Saturday to take "every measure to prevent the disaster from worsening by taking advance actions".