Hundreds of people have been injured, and dozens of homes have been completely destroyed in the disastrous downpours; most of the deaths have occurred in Hiroshima subdivision.
The unprecedented natural disaster has devastated much of Japan's western region and left the country reeling.
In total in southwestern Japan, the death toll has exceeded 150.
Many major highways and rail lines are still closed and tens of thousands of homes in Hiroshima are still without electricity or clean water.
"We want to demonstrate what we have been training for as a center for summarizing and resolving problems such as food poisoning at evacuation centers and secondary damage accompanying prolonged evacuation", said doctor Yoko So, who leads the team of public health experts.
Some 8.63m people across 23 prefectures have been ordered to evacuate.
Abe visited a shelter at an elementary school gymnasium in Kurashiki, a city where more than 40 people died.
Despite orders and advisories to evacuate, which may have been issued too late, some residents appear to have ignored the warnings because they did not know where to go or how to get to safety.
One family sleeping there has had to send their young daughter away to live with relatives, after she became so distressed by the evacuation that she stopped eating. Floodwaters rose so fast they caught the couple by surprise.
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"We will unite and move swiftly to deliver those necessities to the disaster victims by coordinating closely with local government", Abe said.
Almost 2 million people have been asked to evacuate the affected areas. Also, with others still missing, then it is likely that this figure will grow.
In Takehara, mudslides on Saturday crushed homes.
The heavy rainfall stemmed from the remnants of a typhoon that hit south-western Japan last week.
Despite ebbing floods that opened the route to a hospital where almost 100 patients and staff have been stranded, water still swirled through most of the hard-hit city of Kurashiki.
In Kurashiki near Okayama, soldiers were deployed to carry elderly residents from their homes into waiting boats.
Unfortunately her young colt, Earth, was not as lucky and was found dead, according to PJW. Many waited hours to be rescued.
Abe cancelled a planned trip to Europe and the Middle East this week to oversee the emergency response.
Abe visited Okayama on Wednesday to assess the extent of the damage.
Many social media users have criticised their actions.