There were no immediate reports of damage or injuries.
The magnitude-5.2 earthquake was 57 km deep and was centred in Tokyo Bay, near Haneda Airport, the Japan Meteorological Agency said. It struck at 5.49 a.m. (2.19 a.m. IST).
Subway and train service was briefly interrupted for safety checks.
The agency warned that the quake could cause landslides following recent heavy rains.
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