TOKYO — A quarter of a million evacuees began to return home on Monday after torrential rains over the weekend that killed at least 27 people in southern and western Japan and flooded the grounds of the Temple of the Golden Pavilion in Kyoto.

Most of the deaths were on the southern island of Kyushu, where rain fell at a rate of almost four inches per hour, causing flash floods that swept cars off streets and landslides that swallowed homes. Five people were still missing, and at least 3,000 people were isolated by flooding, the authorities said.

The Japan Meteorological Agency warned that more rain may be on the way. The agency said that while the storm’s peak had passed, there was still a possibility of heavy rains and more flooding in some areas. However, the authorities said it now appeared safe for many of those who had fled their homes for school gymnasiums and other evacuation centers to go home.