Two deaths have been confirmed, and a third body is still under investigation, Fukuoka prefecture's Department of Disaster Management said.
Abe, who cut short a trip in Europe, inspected a collapsed railway bridge in Hita city in Oita prefecture and was also going to neighboring Fukuoka, where the latest deaths were confirmed.
The confirmed deaths total 27 so far, 24 in Fukuoka and three in Oita.
Rains from Typhoon Nanmadol ravaged southern Japan last week. The worst-hit areas were in Fukuoka and Oita on Kyushu, Japan's southernmost main island. Widespread flooding and landslides wrecked homes, roads and rice terraces.
Abe had been visiting European leaders after attending the G-20 summit in Germany. He canceled a visit to Estonia, the last leg of his European trip, and returned to Japan one day earlier than planned.
He returned Tuesday and held a meeting with relevant government ministers to discuss the destruction.
During his visit, Abe met with victims at evacuation sites and talked with officials working in the disaster-hit areas.
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