It issued a major tsunami warning for Ishikawa and lower-level tsunami warnings or advisories for the rest of the western coast of the island of Honshu.
NHK said the tsunami waves could keep returning, and warnings were continuing to be aired nearly an hour after the initial alert.
The government was set to hold a news conference later in the day. Reports of damage were not immediately available.
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A tsunami of about three metres high was expected to hit Niigata and other prefectures on the western coast of Japan. Smaller tsunami waves were already confirmed to have reached the coastline, according to NHK.
The area includes a nuclear plant. Tokyo Electric Power Co, the operator, said it was checking for problems but there were no immediate reports of any irregularities.