The city of Kurashiki and the Hiroshima prefecture are among the affected areas. It's also one of the deadliest natural disasters to hit the island nation since an quake struck off the coast of Tohoku in 2011, triggering a massive tsunami that crippled the Fukushima Daiichi Nuclear Power Plant.
The rain set off landslides and flooded rivers, trapping many people in their houses or on rooftops. Three people died at the scene in Ayabe City in Kyoto Prefecture, where two houses collapsed.
In Kurashiki, 2,310 people have been rescued by authorities and the search still continues.
Media captionAbout two million people were evacuated after rivers burst their banks.
Even with the break in rain, officials warned of the possibility of sudden showers, as well as new landslides in the wettest areas.
Roads were closed and train services suspended in parts of western Japan.
To safeguard their workers, some major businesses in the disaster-hit regions have halted production, including at Mitsubishi Motors Corp. and a subsidiary of Toyota Motor Corp.
Some cities within Okayama prefecture saw flooding of almost 30 percent of the total area, while the number of partially or fully destroyed homes nationwide exceeds 10,000.
Dozens of people are still missing, and with the rains finally letting up on Monday, rescue workers were able to reach previously cut-off places where authorities fear more bodies may be trapped beneath debris. One weather official noted that the region has "never experienced this kind of rain before".
In the city of Kurashiki, 500,000 people endured the worst of the flooding, with some forced to climb to the roof of a hospital to await rescue over the weekend.
They were rescued hours later, and returned to the town on Monday, where Ogawa found his telephone, filled with calls from concerned relatives and friends.
"There are still many people whose safety has yet to be confirmed", he added.
Some people were already feeling unwell in the summer heat as they waited in line outside for a water supply truck at an evacuation center in Mihara, Hiroshima Prefecture, despite a portable air conditioning device cooling the spot.
The United Nations said secretary-general Antonio Guterres had written to Mr Abe offering UN support in the clean-up.
European Union chief Donald Tusk has suggested moving the postponed summit with Prime Minister Shinzo Abe to Tokyo next week.
This time, five people who are qualified under the DHEAT system, including doctors and public health nurses from a team in Nagasaki Prefecture, have been dispatched to Kurashiki.
The toll has risen steadily since then, and conditions have made rescue operations hard, with some desperate citizens taking to Twitter to call for help.
Japan mobilized tens of thousands of army troops, police and firefighters to undertake rescue efforts. The Ministry of Land reports that blocked roads and national highways as well as damaged railway tracks affecting 29 rail routes are slowing the distribution of food and supplies from east Japan.