The quake struck at 9:23 pm (local time) in Ibaraki 41 kilometres northeast of Tokyo at a depth of 37 kilometres, the US Geological Survey said, putting the magnitude at 5.4. It was felt in large parts of eastern Japan.
Japanese authorities said there was no danger of a tsunami.
The country sits at the meeting place of four tectonic plates -- part of the so-called Pacific "Ring of Fire" -- and experiences a number of relatively violent quakes every year.
However strong earthquakes last month hit southwestern Japan, killing nearly 50 people.