Thousands of people were told to leave coastal areas for higher ground after the quake in waters off Iwate prefecture, 530km (330 miles) north of the capital Tokyo.
The biggest waves measured 80cm but the meteorological agency in earthquake-prone Japan warned that quakes "causing even stronger shaking" could occur in the next week, producing bigger waves.
Later, the agency warned the risk of a quake measuring 8.0 or higher was now "relatively higher than during normal times".
People in Japan are still scarred by memories of a huge quake in 2011 that triggered a tsunami which killed more than 18,000 people and caused a meltdown at the Fukushima nuclear plant.
After Monday's undersea quake, recorded at a depth of 10km, warnings of possible bigger waves were issued to residents in areas nearest the epicentre - in Japan's main island, Honshu, and the northern region of Hokkaido.
Tremors were felt as far away as Tokyo.
In Hokkaido tsunami alerts remained in place two hours after the quake struck at 16:52 local time (08:52 BST).
