Utility Kyushu Electric Power said a reactor at Sendai, about 1,000 kilometres southwest of Tokyo, started "normal operation at 4 pm (0700 GMT) following final inspections" conducted by the Nuclear Regulation Authority on the day.
The plant reached full power generation at the end of last month and is now ready to supply the Kyushu region.
But the same day an anti-nuclear citizen group submitted a request to close the plant to Kagoshima prefecture where the reactor is located, according to public broadcaster NHK.
The restart came after a quake-sparked tsunami in 2011 swamped cooling systems and triggered reactor meltdowns at the Fukushima plant, prompting the shutdown of Japan's 50 reactors and starting an impassioned public debate over the use of atomic power.
The government temporarily restarted the Oi nuclear reactors in 2012 to prevent power shortage in the central Kansai region, but they stopped operations for inspections in September 2013.
The accident sent radiation over a wide area and forced tens of thousands from their homes -- many of whom will likely never return -- in the worst nuclear accident since Chernobyl in 1986.
