Officials in Ehime prefecture asked the government to review its weather warning system, noting that rain warnings were issued after damage and casualties already had occurred.
In addition to the water outage, people in afflicted areas were plagued with severely hot weather.
Flooding and landslides caused by record rains are believed to have killed more than 100 people, with scores missing.
Chief Cabinet Secretary Yoshihide Suga said more than 50 people were still unaccounted for as of Tuesday afternoon, majority in the hardest-hit Hiroshima area.
Local government officials said pumping trucks were being deployed to help restore access to some of the worst-hit areas, and on Monday flood water was finally starting to recede as the rains stopped.
Around 10,000 people whose homes were buried by landslides or submerged in flood waters are still in shelters.
"We can not take baths, the toilet doesn't work, and our food stockpile is running low", 23-year old nursery school worker Yumeko Matsui tells NBC.
Delivery companies Sagawa Express Co and Yamato Transport Co and cargo service Japan Freight Railway Co said some of their shipments to and from the flooded areas have been suspended or reduced.
Construction worker Fukuyoshi Doi volunteering to get that done, and supervised other volunteers who gathered to help.More news: Stormy Daniels' Ohio Strip Club Charges Dismissed
More than 200,000 households had no water a week after disaster struck and many thousands of people were homeless.
"What we are getting is a thin stream of water, and we can't flush toilets or wash our hands", he added, standing over a 20-litre (4.4-gallon) plastic tank that was only partly filled after nearly four hours of waiting.
At one point during the flooding, evacuation orders were given for almost 6 million people across 19 prefectures. People who have evacuated their homes have since returned and started cleanup.
He is planning to also visit Hiroshima and Ehime prefectures next.
He said the United Nations chief "commended the Government's efforts to help people affected and expressed his admiration for the domestic search and rescue teams helping those in need".
Both emergency services, households and evacuees have struggled with telecommunications services as NTT West said that almost 16,000 landlines and internet connections are down affecting an expansive area of western Japan.
A new evacuation order went out on Tuesday in a part of Hiroshima after a river blocked by debris overflowed its banks, affecting 23,000 people.
With much of the affected area lacking fresh water and electricity and with temperatures and humidity soaring, the dangers of dehydration and water-born infections pose new risks.
On Monday, Prime Minister Shinzo Abe canceled a four-stop overseas trip as the death toll rose, and his office said he would visit Okayama on Wednesday.
Indeed, with the severity of the crisis impacting large swathes of areas in Western Japan and Southwestern Japan becoming understood, then more individuals are now involved in search and rescue.