The northern region of Tohoku felt "a strong jolt" from the quake, which happened at 10:13 pm (1313 GMT), according to the meteorological agency.
The quake was located off the Pacific coast of northern Miyagi prefecture, roughly 350 kilometers (220 miles) northeast of Tokyo.
The quake happened 40 kilometers underground, the agency said.
Although there were no immediate reports of damage or casualties, the quake was strong enough to shake skyscrapers in central Tokyo.
The quake followed a moderate earthquake measuring 4.3 on the Richter Scale that hit central Japan.
The first tremor hit at 9:54 pm (12:54 GMT) about 50 kilometers (31 miles) underground in Saitama prefecture, just north of Tokyo, the agency said.
Japan experiences 20 percent of the world's major earthquakes.