Utility Kyushu Electric is shutting down the No. 1 reactor at its Sendai plant in southern Kagoshima for a few months of inspections and maintenance, leaving Japan with just two operating reactors.
But there is speculation that the reactor's safety work could drag on longer.
Today's shutdown follows demands from the region's top politician that Kyushu Electric conduct extra safety inspections at its two operating reactors in the Sendai plant - after deadly quakes hammered a neighbouring prefecture in April.
But it agreed to what it called "special inspections" in addition to regular maintenance work. Sendai's No. 2 reactor will be shut down for a similar review starting in December.
More From This Section
Dozens of reactors were switched off in the wake of the March 2011 Fukushima accident, the worst nuclear disaster in a generation.
Anti-atomic sentiment still runs high five years later, challenging a push by Prime Minister Shinzo Abe and utility companies to switch Japan's stable of reactors back on.
The catastrophe forced resource-poor Japan to turn to expensive fossil fuels to plug its energy gap, but fears about the safety of nuclear power and radiation exposure linger.
Another reactor has been restarted at the Ikata plant in western Japan.
Opposition to nuclear power has seen communities across the country file lawsuits to prevent restarts, including the Sendai plant.
The residents argued that the plant's operator underestimated the scale of potential earthquakes and volcanic eruptions that could hit the region. A court rejected their argument and ordered restarts.