The epicentre of the earthquake was off the coast of Chiba prefecture, adjacent to Tokyo, the agency said, adding that a tsunami warning had not been issued.
The quake, which hit at 9:16 a.m. (0016 GMT), had a maximum intensity of 4 on Japan's 1-7 scale, including in parts of central Tokyo.
There were no were immediate reports of damage.
Earthquakes are common in Japan, one of the world's most seismically active areas. Japan accounts for about 20 percent of the world's earthquakes of magnitude 6 or greater.