Police and municipal officials said 18 people were injured.
Among the injured was a 49-year-old woman whose index finger was chopped off as a gust slammed a door shut in the southern prefecture of Miyazaki.
The storm was roughly 10km northwest of the city of Izumi, some 600km west of Tokyo, as of 9am (00:00 GMT), the Japan Meteorological Agency said on Friday.
It had winds gusting up to 126kph and was heading north at 30kph.
"The storm is expected to curve east and may bring heavy rain to Niigata on Saturday, so people have to be alert for the chances of landslides and other damage," an agency official said.
Last month, Typhoon Man-yi struck Kyushu and killed three people, injured more than 70 and flattened several houses.