TEPCO said it managed to restart the system some 90 minutes after the failure.
The cooling system servicing the Unit 3 spent fuel pool was not able to circulate water to cool the nuclear fuel because of a broken pump, according to the Nuclear Regulatory Agency.
The exact cause of the cooling system stoppage is currently unknown.
However, the system might have been “shaken” during the earthquake, according to nuclear agency officials, as reported by NHK.
The station’s storage pool currently contains 2,544 spent fuel rods.
No cooling water leaks or any other “abnormalities” have been reported.
Tsunami waves of up to 1.4 metres have hit the Japanese coast after a strong earthquake struck offshore early on Tuesday morning.
A tsunami warning was downgraded to an advisory for Fukushima and Miyagi prefectures on the Pacific coast of northeastern Japan.
The same region was struck by a devastating tsunami in 2011.
The highest tsunami so far was recorded at Sendai Bay about two hours after the earthquake.
The Japan Meteorological Agency has recorded smaller waves along the coast.
It warned that waves of up to 3 metres could reach Fukushima and Miyagi prefectures.
The earthquake, which was felt in Tokyo, was centred off the coast of Fukushima prefecture at a depth of about 10 km, the the Japan Meteorological Agency said.