The magnitude 6.9 temblor hit at 6:39 a.m. (2139 GMT) and was centered off the coast of Sanriku in northern Japan, the agency said. The U.S. Geological Survey put the magnitude at 7.2.
There was no immediate explanation for the discrepancy. The quake hit at a depth of about 24 kilometers (15 miles), the U.S. agency said.
The Japanese agency said the tsunami could be 50 centimeters (19.5 inches) high and could reach Japan's Pacific Coast between 7:10 a.m.(2210GMT) and 7:30 a.m.(2230 GMT). Such waves are often barely noticeable in the ocean but can rise to greater heights once they arrive at shore.
There were no immediate reports of injuries, according to national broadcaster NHK, AP reports.
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