About 900 mm of rain has fallen on the southernmost main island of Kyushu since late June, with heavy rain forecast to continue into Thursday.
Japan ordered nearly 800,000 people on the southern island of Kyushu to take shelter in evacuation centres and other safe areas on Wednesday as heavy rains threatened to trigger landslides and cause other damage.
Some parts of southern Kyushu have received up to 1,000 millimetres (39.4 inches) of rain since Friday, and forecasters expect as much as 350 mm to fall in some areas by midday on Thursday, Japan's public broadcaster NHK said.
Evacuation orders were issued for nearly 600,000 residents of Kagoshima city and two smaller cities in the same prefecture, the broadcaster said.
Another 310,000 residents of the island were advised to find shelter, Kyodo News reported.
In Tokyo, Prime Minister Shinzo Abe said residents should "take steps to protect their lives, including early evacuation" and he ordered the military to prepare for rescue operations if needed.
Abe was criticised for the government's slow response last July when heavy rains triggered landslides and floods, killing more than 200 people in Japan's worst weather disaster in 36 years.