Heavy seasonal rains last week caused severe flooding that tore up roads and destroyed houses on Japan's southernmost island of Kyushu, with hundreds of thousands of people forced to flee their homes.
At least 25 people have been confirmed dead while more than 20 were still missing on Wednesday.
A week after the disaster began, hundreds of people were still staying in school gymnasiums and public buildings used as makeshift shelters.
More than 10,000 rescuers, including soldiers, battled through thick mud with little hope of finding survivors.
Public broadcaster NHK showed footage of rescuers shoveling mud and removing washed up driftwood from what seemed to be roads and farm fields.
Abe, who cancelled a visit to Estonia that was originally planned as the last leg of a European tour, flew to the region to view the damage and console residents.
Clad in blue work clothing, Abe told evacuees in a shelter that the government was working to restore the region.
Abe later met with Oita prefecture governor Katsusada Hirose, Kyodo News reported.
"I was once again reminded of the severe level of damage after seeing with my own eyes the sites hit by torrential rain and mudslides," Abe told Hirose, pledging that the central government will work "to improve conditions at evacuation centres and secure housing".
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