In the city of Hiroshima, "we have issued a special heavy rain warning. This is a level of heavy rain that we have never experienced before", the JMA said in a statement.
The land ministry warned that water levels are extremely high in three rivers–two running through the Hiroshima region, and one in southern Kumamoto.
Scientists say climate change is intensifying the risk of heavy rain in Japan and elsewhere, because a warmer atmosphere holds more water.
On Friday, the JMA said that in the 24 hours from 6am on Friday, 300 millimetres of rain is expected in the northern part of Kyushu, with 200 to 250 millimetres forecast in many other parts of the country.
News from Shimla of India stated that at least 2,000 people were evacuated on Friday after a massive landslide in India's ecologically fragile Himalayan north blocked a major river, officials said.
The people were evacuated from 13 villages in the Lahaul area of Himachal Pradesh state as a "preventative measure" in case of flash floods, a senior district official told AFP.
Hundreds of tonnes of rocks and other debris slid into and partially blocked the Chenab–one of the biggest rivers in the region–blocking the flow of water for a few hours.
This is the second landslide to hit the northern state bordering Tibet this week.
On Wednesday, 12 people were killed after a bus and other vehicles travelling on a road were buried by rocks and mud.
Sixteen people are still unaccounted for, according to local media reports. Thirteen others were pulled out of the rubble.
Experts blame climate change besides construction work on hydroelectric dams and deforestation for causing the catastrophe.
In February, a ferocious flash flood hurtled down a remote valley in neighbouring Uttarakhand state, killing around 200 people.