According to the agency, the typhoon hit Akune city in Kagoshima Prefecture in southwest Kyushu region, Xinhua reported.
The agency has warned of heavy rains over Shikoku Island.
Due to strong winds, parts of western and northern Japan would also be affected in the coming days.
The meteorological agency has also warned of landslides.
Evacuation orders have been issued to residents in Miyazaki, Kumamoto and Kagoshima prefectures in the Kyushu region.
According to officials, a 12-year-old boy died in Nagano Prefecture Wednesday due to a landslide and an elderly man was killed after falling into a swollen river in Fukushima Prefecture which was hit by heavy rain.