In the hour through 4 p.m., Land Ministry rain gauges recorded 46 millimeters in Ebino City, Miyazaki Prefecture, and 45 millimeters in Kagoshima City.
Weather officials urge people to be on high alert for landslides and flooding, and to keep up to date on the latest information and evacuation orders issued by local governments.
The risk of landslides is extremely high in Kagoshima and warnings have been issued for some areas.
Even if the rain eases, conditions will remain dangerous as the ground has already been loosened and water levels are high. Even a small amount of additional rain could lead to landslides.
Street closure in Miyazaki
Officials in Takachiho Town, Miyazaki Prefecture, say they received a report from police at around 5:30 a.m. that a landslide had blocked a national road in the town's Shimono District.
A slope collapsed from a height of about 10 meters, covering a 200-meter section of the road with mud and concrete. Six other locations, including prefectural and town roads, are also closed to traffic due to landslides and fallen trees.
Temple destroyed in Kumamoto
A temple in Mashiki Town, Kumamoto Prefecture, was crushed by a landslide. None of the temple's walls or columns are visible in footage taken by an NHK viewer. Police say the chief priest and his family had already been evacuated and no one was injured.
Heavy rain warning in place for Kumamoto and other areas of Kyushu
NHK World's meteorologist Tsietsi Monare has more on the record rain that continues in parts of southwestern Japan.
Torrential rain in Kumamoto
The Meteorological Agency says radar analysis shows that about 110 millimeters of torrential rain fell near Uki City, Kumamoto Prefecture, in the hour through 12:00 p.m.
Agency officials urge residents to take measures to protect their safety as there is an imminent risk of disaster.
Officials have issued landslide alerts for some areas in Fukuoka, Saga, Kumamoto, Oita, Miyazaki and Yamaguchi prefectures.
Some rivers in Kumamoto rise above flood risk level
Kumamoto Prefecture officials say water in the Shirakawa and Mifune rivers has exceeded the flood risk level, as of 10 a.m.
This follows an announcement at 7 a.m. that the Kiyama River in Mashiki Town had overflowed its banks. A still photo captured water flooding roads near the river.
Weather officials say developed rain clouds have been hovering over Kyushu and other areas since Sunday night, bringing the risk of landslides, floods, lightning and tornadoes.
The Meteorological Agency issued an extreme rain alert at around 6: 30 a.m. on Monday for Kumamoto Prefecture. But the downpours are now falling mostly in Saga Prefecture, with Takeo City recording 58 millimeters in the hour through 9 a.m.
The officials expect the front to remain in the area until tomorrow around noon, bringing more than 50 millimeters of rain per hour to Kyushu and Yamaguchi Prefecture.