"Evacuate immediately from coastal regions and riverside areas to a safer place such as high ground or an evacuation building," the agency said, adding that property damage was expected.
"Do not leave safe ground until the warning is lifted," the JMA said.
The agency recorded an 80-centimeter (32-inch) tsunami following the earthquake.
Shinkansen bullet train services between Tokyo and Aomori, the northernmost city on Japan's largest island of Honshu, have been suspended for the time being.
