The Japan Meteorological Agency said the quake in southern Ibaraki, east of Tokyo, had a depth of 50 kilometres (30 miles).
No damage or injuries were immediately reported, but bullet trains suspended operations between Tokyo and Koriyama in northeastern Japan's Fukushima region due to a power outage, NHK reported.
Hiroyuki Sanada, an official at the Nuclear Regulation Authority, said "no abnormality" had been reported at the Tokai Daini nuclear plant in Ibaraki, which was halted for safety checks.
Japan experiences around 1,500 jolts every year, accounting for about 18 percent of the world's earthquakes. The vast majority are mild.
Despite strict building guidelines, many structures, particularly outside major cities, are old and vulnerable.
This was brought home by this year's 7.5 magnitude New Year's Day quake, which hit the Noto Peninsula and killed more than 230 people, many of them when older buildings collapsed.
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