Almost 70 reportedly died in the hardest-hit Hiroshima area alone.
More than 20,000 people were killed or went missing during the 2011 disaster, when a 9.0-magnitude quake hit Japan, triggering a tsunami and nuclear meltdown at the Fukushima nuclear plant.
The flooding became severe as much of the rainfall occurred over a mountainous region and trickled down to the plains, causing heavy flooding.
She said one resident had seen a horse swimming through the floodwaters later that day.
Authorities said that 85 people are dead, 6 are in critical condition and at least 58 are missing, according to Japanese broadcaster NHK.
In Kumano, a mountainside community in Hiroshima prefecture that was hit by a landslide last week, Ken Kirioka anxiously watched rescuers toiling through mud, sand and smashed houses to find the missing, including his 76-year-old father, Katsuharu. "We recognize that there's a need to look into steps we can take to reduce the damage from disasters like this even a little bit", he added.
Alongside the spiraling death toll from the torrential downpours, floods and landslides which struck parts of central and western regions nearly a week, some five million people have been forced to evacuate and millions remain displaced.
While persistent rain had ended, officials warned of sudden showers and thunderstorms as well as more landslides on steep mountainsides saturated over the weekend.
The Japan Meteorological Agency had lifted all special rain warnings issued in 11 prefectures by Sunday, and is calling for caution regarding sediment-related disasters in the coming days. Rivers overflowed, turning towns into lakes and leaving dozens of people stranded on rooftops.
Hundreds of homes have been destroyed or damaged.
"We will firmly set fiscal measures to help local governments deal fully with the emergency situation and the recovery with a sense of security", said Prime MinisterShinzo Abe.
At least 4 million people have been advised to evacuate surrounding areas. The bodies of a fourth-grade boy at an elementary school and his mother were found, two of three family members who went missing due to landslides in Uwajima, Ehime Prefecture.
The footage also showed Japanese soldiers rescuing children by boat from a flooded river in Hiroshima.
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