Fifty-six millimeters of fresh rain fell between 2 a.m. and 3 a.m. on Sunday in Yakushima Town in southern Japan.
The area received more than 400 millimeters of rain in a 12-hour interval on Saturday. This was as much rain as the town in Kagoshima Prefecture would normally have in all of May.
Weather officials warn of the risk of mudslides because of the intermittent heavy rain.
The Meteorological Agency says this much rain is a once in 50-year event.