Kansai Electric Power Co (KEPCO), the largest utility firm after Tokyo Electric Power Co (TEPCO), began lowering power generation in unit three at the Takahama nuclear plant in Fukui prefecture, a KEPCO spokeswoman said.
The reactor is expected to be disconnected completely by midnight, leaving all 11 reactors around the country owned by KEPCO idle, she said.
The move comes on the day that Japan announced a record trade deficit in January as fuel imports soared for the resource-poor nation following the nuclear disaster at the Fukushima Daiichi plan in March.
Before the accident, which was caused by a deadly earthquake and tsunami, Japan had relied one third of its power supply on nuclear energy.
But power companies including KEPCO, which provides electricity to the major western cities of Osaka, Kyoto and Kobe, have not been able to resume reactors after inspection due to the safety concerns of local residents.
Once the Takahama reactor goes offline it will leave one unit operational at TEPCO's Kashiwazaki-Kariwa plant in central Japan and one at the Tomari plant in northern Hokkaido.
Those two units are expected to be closed down for inspection by late April.