Typhoon Malakas made landfall in the southernmost main island of Kyushu shortly after midnight (1500 GMT), packing winds of up to 180 kilometres (112 miles) per hour, the Japan Meteorological Agency said.
Television footage from public broadcaster NHK showed houses, cars and rice fields partly covered in the muddy brown water in Miyazaki prefecture, where a record 578 millimetres of rain fell on one city in just 24 hours.
A woman in her 30s was slightly injured when strong winds broke a window at her house and six people had to be rescued from their waterlogged homes by boat, but no serious injuries or deaths have been reported.
According to NHK, 106 flights have been cancelled because of strong winds, as the typhoon moves northeast toward Tokyo with officials warning of high seas, possible landslides and more flooding.
At least 17 people died earlier this month when Typhoon Lionrock slammed into the country, which is regularly struck by big storms.
Before Lionrock, two typhoons had claimed at least two lives in Japan's northeast.
In 2013 a powerful typhoon that triggered massive landslides on Oshima island killed 40 people, while 82 died after a typhoon hit Japan in 2011.