For southern Kyushu, the JMA predicted an enormous 1,100mm of precipitation in the 48 hours to Friday morning.
Video on public broadcaster NHK TV showed roof tiles being blown off houses, broken windows and felled trees.
“Our carport roof was blown away in its entirety. I wasn’t at home when it happened, but my kids say they felt the shaking so strong they thought an earthquake happened,” a local resident in Miyazaki told NHK.
“I was surprised. It was completely beyond our imagination,” she said.
Auto giant Toyota has suspended production at all 14 of its factories in Japan.
Japan Airlines cancelled 172 domestic flights and six international flights scheduled for Wednesday and Thursday, while ANA nixed 219 domestic flights and four international ones on Wednesday, Thursday and Friday.
The cancellations affected around 25,000 people.
Kyushu Railway said it would suspend some Shinkansen bullet train services between Kumamoto and Kagoshima Chuo from Wednesday night and warned of further possible disruption.
Trains between Tokyo and Fukuoka, the most populous city on Kyushu, may also be cancelled depending on weather conditions this week, other operators said.
Shanshan comes in the wake of Typhoon Ampil, which disrupted hundreds of flights and trains this month.
Despite dumping heavy rain, it caused only minor injuries and damage.
Ampil came days after Tropical Storm Maria brought record rains to northern areas.
Typhoons in the region have been forming closer to coastlines, intensifying more rapidly and lasting longer over land due to climate change, according to a study released last month.
