Japan Nuclear Fuel Limited reported the problem at a plant compound in Rokkasho Village on Sunday. It says the glitch poses no threat to the environment.
The operator says one of the tanks storing radioactive waste lost its cooling functions for about eight hours from around 3:30 p.m.
About 2,600 liters of waste liquid produced during a test operation was stored in the tank.
The operator says it found cooling water levels dropping at around 7 p.m. on Saturday. An inspection discovered that the valve of a circulating water piping system had been turned off for some reason.
The operator said the temperature of the waste liquid briefly rose to 32 degrees from the usual 24 degrees. It says there is no leakage of radioactive substances.
The operator said it officially confirmed at 2:26 a.m. on Sunday that the cooling function had stopped working, explaining why it announced the problem one day after it occurred.
The Aomori prefectural government has dispatched officials to the plant and urged the operator to determine the cause of the problem and come up with measures to prevent a recurrence.