The agency had asked the operators to submit plans on how to improve their readiness to handle emergencies after Tokyo Electric (Tepco), came under criticism in the wake of the 6.8-magnitude quake which killed 11 people and injured more than 1,000.
The quake triggered a small fire at Tepco's Kashiwazaki Kariwa plant – the world's largest in terms of capacity - in Niigata.
It took two hours to put out the fire because plant officials had trouble notifying fire officials, Tepco said.
In the following days, TEPCO announced a barrage of leaks and malfunctions.
Ryo Shimizu, a spokesman for the utility company, confirmed on Thursday that 30 tonnes of rainwater had leaked into four buildings at the plant, after heavy rains hit the region.
The water was believed to have leaked inside through gaps made by the quake, he said, adding that the water contained no radioactive materials.