The 6.1 magnitude quake happened around 6.30am (local time) and is said to be an aftershock of the huge quake which initially triggered tsunami warnings.
The tremor occurred 37km south of Namie, according to the Japan Meteorological Agency with four similar quakes measuring between 4.6 and 3.8 magnitudes following within half an hour.
No tsunami warning has been issued yet.
Warnings of waves up to 10ft high were issued at around 21:00 GMT on Monday night with tsunami sirens and alerts being set off.
Thousands were called to evacuate areas across Japan’s eastern coast and minor injuries were reported.
In 2011 an earthquake and subsequent tsunami struck the region killing 18,000 people and set off a meltdown at the Fukushima nuclear power plant.
Waves around 4.5ft were spotted washing ashore around Sendai – which is roughly 45 miles
north of Fukushima.
A resident of Iwaki, a city close to Fukushima, said: “We saw high waves – but nothing that went over the tidal barriers.”
The Japanese Meteorological Agency ordered several locations to “evacuate immediately” and move to higher ground as news of the tsunami broke.
An emergency bulletin stated: "Tsunami Warning. Damage due to tsunami waves is expected.
"Evacuate immediately from coastal regions and riverside areas to a safer place such as high ground or an evacuation building.
"Tsunami waves are expected to hit repeatedly. Do not leave safe ground until the warning is lifted.
"Get out of the water and leave coastal regions immediately.
"Due to the risk of ongoing strong currents, do not enter the sea or approach coastal regions until the advisory is lifted."