The damage has spread beyond Kyushu into central Japan's scenic mountain villages known for hot springs and hiking.
Japan's Fire and Disaster Management Agency said rising floodwater or roads damaged by landslides had blocked access to more than 3,000 households.
Though the rains were causing fresh flooding threats in central Japan, flooding was still affecting the southern region.
Pounding rain since late Friday in Japan's southern region of Kyushu has triggered widespread flooding.
Army troops and other rescuers worked their way through mud and debris along the flooded Kuma River, where many houses and buildings were submerged nearly to their roofs.
The maximum number will be 5,000 or 50% of the stadium capacity, whichever is smaller.
Large areas along the Kuma River were swallowed by floodwaters with many houses, buildings and vehicles submerged almost up to their roofs.
More than 75,000 residents in the prefectures of Kumamoto and Kagoshima were urged to evacuate following pounding rains overnight.
The latest rise began in late June, weeks after Japan lifted a state of emergency that allowed Tokyo to gradually return to business.
The unusual move appeared to have broad support from citizens both young and old, with very few people on the streets of Yamato spotted breaching the new rule.
Pierre Ducrey, the Olympic Games operations director, has called the Athletes Village “problem No. 1."
Megumi disappeared in 1977 on her way home from her a junior high school in Niigata on Japan's northern coast when she was 13.
But the roughly 900 deaths, or 7 per million people, in Japan are far fewer than the 320 per million in the U.S. and more than 550 per million in Italy and Britain.
Japan, with about 16,600 confirmed cases and about 850 deaths, has so far avoided the large outbreaks that have been experienced in the US and the Europe despite its softer restrictions.
The state of emergency was originally scheduled to end on May 6, and the government extended it through May 31.