Utility Kyushu Electric Power said it restarted the number-two reactor at Sendai, about 1,000 kilometres (620 miles) southwest of Tokyo at 10:30 am (0130 GMT).
The same power plant's number-one reactor was restarted in August, ending a two-year nuclear power hiatus.
Engineers will now spend several days bringing the newly restarted reactor up to operational level before running it commercially from November.
The restart comes more than four years after a quake-sparked tsunami swamped cooling systems and triggered reactor meltdowns at the Fukushima plant, prompting the shutdown of Japan's 50 reactors and starting a pitched battle over the future use of atomic power.
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But the public is largely opposed to atomic energy after the Fukushima crisis 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.
The government will continue to restart reactors that are deemed safe under the nation's standards, upgraded since the Fukushima accident in 2011, said Chief Cabinet Secretary Yoshihide Suga.
"There is no change to this policy of the government," Suga told a press conference.
"Many people are still concerned about the restart of nuclear power plants," Ryoko Torihara, head of the citizen group against the Sendai nuclear plant, told NHK.
Campaign group Greenpeace criticised "the Abe government's disregard for public safety," and argued that Japan has demonstrated that it does not need nuclear power.
"Nuclear energy will not make any significant contribution to Japan's energy mix -- not now or in the foreseeable future," said Mamoru Sekiguchi, energy campaigner at Greenpeace Japan.