The 91 people mainly suffered from cuts and bruises from broken glasses and falling objects and none of the injuries was life threatening, a National Police Agency official said.
The earthquake caused strong shaking of up to 40 seconds in many areas of northern Japan and was strong enough to shake buildings in the heart of the capital, Tokyo.
There were no immediate reports of any problems at the nearest nuclear power plant, which continued operations, according to local media reports.
But Japan's "bullet" high-speed trains were suspended in some areas, according to operator East Japan Railway.
The earthquake also triggered landslides at several locations, the police agency official said.
Shinya Izumi, the minister overseeing disaster response, told reporters the quake left about 6,700 homes without electricity.
A 6.8 magnitude earthquake is capable of causing serious, widespread damage.
Last month, a 7.2-magnitude earthquake struck sparsely populated rural areas in northern Japan, killing at least 12 people, leaving 10 others missing and injuring more than 300.
Takashi Yokota, a Meteorological Agency official, warned of possible aftershocks from Thursday's quake.