Dozens of people remain missing and more than 200,000 households are without water, the government said on Thursday.
More than 70,000 rescuers are involved in operations to search for missing people across parts of western Japan where the downpours fell.
The worst affected areas are said to be Hiroshima, Kyoto, Okayama and Ehime.
Although dry and hot weather is expected to prevail in the coming days, survivors are at risk from heat-related illnesses and a lack of clean water.
Temperatures are expected to hit between 31C and 34C (86F to 93F).
Why have so many people died?
The deadly flooding began on July 5 and was caused by unprecedented heavy rain at the end of June, worsened by Typhoon Prapiroon, which made landfall on July 3.
Japan flooding 2018 map: Where did the rains hit?
Disaster experts are now warning climate change could fuel more torrential rain in the future.
Takashi Okuma, an emeritus professor at Niigata University who studies disasters, said: “The government is just starting to realize that it needs to take steps to mitigate the impact of global warming.”
Many of the communities hit were in mountain slopes and flood plains previously untouched by heavy rainfall but dozens of people were killed in a similar disaster last year.
Chief Cabinet Secretary Yoshihide Suga told a news conference in Tokyo. “It’s an undeniable fact that this sort of disaster due to torrential, unprecedented rain is becoming more frequent in recent years.”
Japan flooding 2018 map: Western Japan already battered by heavy rains now faces extreme heat
Risk areas unmapped
Since 2005, districts have been required to create and raise awareness of “hazard maps” for areas at risk of landslides and flooding.
But many experts say buildings were built in hazardous areas prior to this, meaning people may have missed or not been alerted about evacuation procedures during last week’s disaster.
Kenji Ishii, a 57-year-old resident of Mabi district, who lived in one of the at-risk areas said he “did not know that very well”.
Japan flooding 2018 map: Hiroshima has been badly hit
Japan flooding 2018 map: Areas in western Japan are worst affected
Japan remains unprepared for flood warnings
Being situated along the edge of the Ring of Fire, Japan is well-versed in earthquake preparation.
But this does not extend to flood disaster prevention, according to Mr Okuma.
Following smaller-scale floods in recent years, the Ministry of Land, Infrastructure, Transport and Tourism has now pledged begun drafts for planning procedures.