"We are afraid that people may not be able to evacuate due to strong wind or floods blocking evacuation routes," said Hiroshima's governor, Hidehiko Yuzaki.
"I would like people to evacuate in advance so that they can save their lives."
Evacuation advisories have been issued to 36,400 people in the western city of Shobara, and 6,300 in the city of Kure, Japanese media report.
The prefectures worst hit by flooding were Okayama, Hiroshima and Yamaguchi, in the Chugoku region, and more than 4,000 survivors are still living in temporary shelters there.
"We are fully ready 24 hours a day to evacuate residents," Tadahiko Mizushima, an official in Okayama, told the AFP news agency.
"We are paying special attention to the areas where restoration of river banks is under way as it would be the first heavy rain since the disaster."
"It's going to deal a double punch," one Okayama man told Japan's public broadcaster NHK. "We are seriously worried."
Sandbags are being rapidly deployed as barriers against the feared flooding.
Images already show sizeable waves off the coast south-west of Tokyo, and ferry services are suspended. Forecasters say the area around the capital could see 40cm (15in) of rain in 24 hours from noon on Saturday.
The floods earlier in July were Japan's worst weather disaster in decades, and were swiftly followed by an unprecedented heatwave which has been declared a natural disaster.