He said that eight others were hurt in the earthquake, one seriously.
A 5.6 magnitude aftershock followed the main quake.
NHK flashed an alert moments before the quake struck, as part of a new warning system.
The country's high-speed 'bullet' trains were shut down as a precaution.
"It was scary. It was difficult to stand up," Sachiko Sugihara, a store worker in the town of Oshushi in Iwate prefecture, told NHK.
Sendai, the nearest large city to the earthquake's epicentre, appeared to be unaffected by the tremor.
"So far we have not received any reports of damage or injuries. Everything is normal," Hideki Hara, a police official in Sendai, said.
"Phone lines, water and electricity are all working right now."
Japan experiences about one-fifth of the world's earthquakes and its infrastructure has been designed to withstand such eventualities.