Most injuries occurred either due to strong wind outside or due to broken windows inside buildings, according to the NHK broadcaster.
Thousands have already been evacuated, while tens of thousands of households have had their power cut.
In Kyoto, a fire was bolstered by the strong wind, spreading across 12 buildings. Local authorities are warning the residents about the danger of new landslides.
The storm with winds of 144 kilometers per hour (89 mph) was previously expected to come close to Chiba prefecture on Honshu before making landfall to the west on Saturday night or Sunday morning.
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Japanese officials have warned of severe swells, landslides and flooding, especially in western parts of the country that were devastated by heavy rains earlier this month.