The quake occurred at 10.22 p.m. on Tuesday and had its epicenter at sea - though near the coast - close to the border that separates the prefectures of Niigata and Yamagata, reports Efe news.
As soon as the seismic activity was registered, the Japanese Meteorological Agency (JMA) issued a tsunami alert that was lifted three hours later.
The tsunami's waves could be seen in Awashima, Sakata, Sado, Wajima and Niigata, where they reached a maximum height of 0.1 metres (less than four inches), according to the agency's data.
Japanese authorities were still checking the state of buildings, although no serious structural damage to residences or installations has so far been identified.
The JMA has urged people in the affected area to remain alert due to the risk of building collapses and landslides as similar tremors and aftershocks may still occur and in light of the rains forecast for Wednesday in part of the region.
The quake led to the temporary closure of some roads and interruptions in rail services, but no accidents were reported.
Some 10,000 people were affected by the shutdown of the bullet trains, although the popular commuter service has since been restored.
Japan sits on the so-called Ring of Fire in the Pacific Ocean, one of the world's most seismically active areas.
( With inputs from IANS )