According to the meteorological agency in Tokyo, the quake, measuring 5.0 on the Richter scale, struck the capital and other eastern Japanese areas on Wednesday at 07:30 GMT.
The tremors were powerful enough to make tall buildings in central Tokyo shake noticeably for several seconds.
The focus of the quake was 80km under the northeast coast of the Tokyo Bay, about 30km east of the capital's downtown area. No tidal wave warning was issued.
At least three people were injured in the capital in quake-related accidents, the Tokyo Fire Department said.
"One of them, a 74-year-old woman, was seriously injured as she fell on the stairs from the second floor of her house," said a fire department representative.
Public broadcasting network NHK said two others were also injured in Chiba, east of Tokyo.
Shinkansen bullet train services were temporarily suspended near Tokyo due to an automatic shutdown in electricity supply, officials said.