The agency first issued the warning to the city of Tamana and the town of Nagasu at 12.20 am. It later expanded it to include the cities of Yatsushiro, Uki, Kamiamakusa, and Amakusa, as well as the town of Hikawa.
The emergency warning was downgraded to a heavy rain warning for all areas at 3.45pm after the intensity of the rain waned.
A man was found in cardiac arrest in the town of Kosa after his car was struck by a landslide, according to the prefectural government. In Yatsushiro, a woman in cardiac arrest was discovered in a car that had sunk in an irrigation canal. Five people went missing after being swept away by rivers in Kumamoto and neighbouring Fukuoka Prefecture.
Tamana recorded 404.5 millimetres of rain in the 12 hours until 8.10am, while Yatsushiro had 385.5 millimetres in the 12 hours until 10.50am, both record highs for those locations.
"Even a little more rain will increase the risk of disasters in Kumamoto," Shuichi Tachihara, director of the meteorological agency's Forecast Division, said at a press conference in Tokyo.
Prime Minister Shigeru Ishiba instructed officials to respond to the heavy rain by putting human life first.
Kyushu Railway Co., or JR Kyushu, fully suspended operations on the Kyushu Shinkansen high-speed train line on Monday morning due to heavy rain.
[Copyright The Jiji Press, Ltd.]