In Hiroshima Prefecture, a 12-meter section of riverbank on the Inokogawa River in the city of Fukuyama collapsed, causing minor injuries to two people.
Fukuyama was hit by 148.5 millimeters of rain (almost the entire month of June average) from midnight through 6 a.m. Thursday.
In the 24 hours to 6 a.m. Friday, rainfall was expected to reach 120 mm in some locations in Shikoku and the Kinki western region of Japan, and 100 mm in the Izu islands off Tokyo, according to the Meteorological Agency.
The agency advised residents in Kyushu to remain alert for landslides.
According to West Japan Railway Co., a four-car train running on the JR Sanyo Line between Seno Station in the city of Hiroshima and Hachihonmatsu Station in the city of Higashihiroshima derailed about 12:35 a.m.
Thursday because of a mudslide on the tracks. Some 150 passengers were on the train, but no injuries were reported.
Part of the first car of the train came off the tracks in Hiroshima's Aki Ward.
The driver of the train applied the emergency brake after noticing the landslide, but to no avail, according to the Hiroshima branch of the railway operator.
The amount of rain in Hiroshima totaled 101.1 mm in the 24 hours to 7:30 a.m. Thursday, the Meteorological Agency said.
In Kurume, Fukuoka Prefecture, Takenori Nonaka, an 86-year-old farmer, went missing after he went to check his rice fields early Wednesday morning.
Police said he may have fallen into a swollen waterway and got swept away.
Yu Matsuura, a 19-year-old university student who disappeared Tuesday while swimming, was found dead Wednesday in a river in Nobeoka, Miyazaki Prefecture, police said.
An hour's rainfall amounted to 51.5 mm by around 1:25 a.m.
Thursday in Iwakuni, Yamaguchi Prefecture, 39.0 mm by around 2 a.m. in Kure in neighboring Hiroshima, and 46.5 mm by around 3:40 a.m. in Hirakata, Osaka Prefecture.
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