The Japan Meteorological Agency says the tremor which shook Tokyo and surrounding areas on Thursday night was smaller in scale than a major earthquake which could occur directly beneath the capital.
The government's Earthquake Research Committee says there is a 70 percent chance of an earthquake with a magnitude of 7 occurring within 30 years directly beneath Tokyo.
The Cabinet Office estimates that such an earthquake could register an intensity of seven on the Japanese seismic scale of zero to seven in Tokyo. It says the death toll could be about 23,000 in a worst case scenario.
The Meteorological Agency says the latest earthquake had a magnitude of 5.9, and recorded an intensity of five plus on the Japanese scale in Tokyo and Saitama Prefecture.
An agency official, Tsukada Shinya, said the potential major earthquake is expected to have a shallower focus and greater magnitude than the tremor on Thursday.