Heavy rain in western Japan forced Kyushu Railway Co.to temporarily suspend shinkansen bullet train services between Kumamoto and Kagoshima on Tuesday afternoon, while delays occurred on trains between Hakata and Kumamoto.
Last July about 200 people died in western Japan in the country's worst flooding disaster in decades.
Torrential downpour has soaked parts of southern Kyushu since June 28.
As of early evening in Japan, authorities had issued evacuation orders for 1,123,000 people in parts of two prefectures: Kagoshima and Miyazaki.
More than a million people on the southern Japanese island of Kyushu were ordered to evacuate as heavy rains continued to lash the region.
"The sound of the rain is so strong that it worries me", one evacuee said.
At 11:10 a.m., the city of Kirishima, also in Kagoshima Prefecture, switched from an evacuation advisory to an evacuation order, targeting 125,000 residents of 61,000 households.
The southwestern Japan city specifically called on residents in areas close to cliffs, rivers and other risky areas to immediately flee to safer places, the Mainichi Shimbun reported.
Members of the fire department monitor the water level of the Wada River in heavy rain Wednesday, July 3, 2019, in Kagoshima City, southwest Japan.
The rain is causing extensive flooding.
He also urged residents to use caution and try to evacuate early "to protect your lives" rather than waiting until the last minute.
Those affected in Kagoshima and Miyazaki prefectures were brought to emergency shelters and higher ground after over 1,000 mm (39.4 inches) of rain pummeled the area since Friday.
The annual rain front is expected to remain stationary between western and eastern Japan through Friday, and some parts of western Japan could get a month's worth of rain in the 24 hours from Wednesday morning through Thursday, according to the agency.
Heavy rain is forecast to continue into Thursday.