The meteorological agency said the quake hit at 11:45 a.m. local time Wednesday and was centered about 90 miles (150 kilometers) off the northeastern coast -- about 270 miles (440 kilometers) northeast of Tokyo -- at a depth of about 6.2 miles (10 kilometers).
A 24-inch (60-centimeter) tsunami reached the coastal town of Ofunato, in Iwate prefecture, shortly after noon. The meteorological agency warned that a tsunami of about 20 inches (50 centimeters) would hit the coast.
The Pacific Tsunami Warning Center in Hawaii said a Pacific-wide tsunami was not expected.
"We have confirmed that small tsunami have come up on the shores, but we have no reports of damage at this point," said Shinobu Nagano, an emergency and disaster response official in Iwate prefecture. "We are still trying to determine the impact of the quake."
Some train lines in the area were temporarily stopped after the quake, but they were restarted shortly after noon.
There was a 6.3 magnitude aftershock shortly after the main quake, the meteorological agency said.
The U.S. Geological Survey said the 7.2-magnitude quake struck 8.8 miles (14.1 kilometers) underground, some 104 miles (168 kilometers) east of the closest major city of Sendai. The two agencies often have slightly different numbers.
Japan lies on the "Ring of Fire" -- an arc of earthquake and volcanic zones that stretches around the Pacific Rim and where about 90 percent of the world's quakes occur.