The move will leave the world's third largest economy without atomic energy for the second time since the Fukushima nuclear crisis erupted in March 2011.
Nuclear power supplied about one-third of the resource-poor nation's electricity before a tsunami knocked out cooling systems and sparked meltdowns at Fukushima, causing tens of thousands to flee their homes.
Prime Minister Shinzo Abe has openly supported a return to the widespread use of atomic energy, but the public remains largely opposed on safety grounds.
"The work started at 4:40pm (0740 GMT)," said a company spokesman. "The reactor will come to a complete stop early tomorrow (Monday)."
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Japan previously was without any nuclear energy in May 2012, when all of the country's 50 commercial reactors stopped for checkups in the wake of the disaster.
Utilities were unable immediately to restart them due to public opposition.
It was the first time in more than four decades that Japan had been without nuclear power.
Their fears proved unfounded but the government last year gave Kansai Electric approval to restart No 3 and No 4 reactors at the Oi plant, arguing that nuclear energy was necessary to meet increased electricity demand during the winter.
The reactors were reactivated in July 2012 and resumed full commercial operation the following month, but the No 3 reactor was shut down earlier this month for a scheduled inspection. The nation's other reactors have remained idle.
The central government and utilities will seek the consent of local governments and communities hosting nuclear plants before any future restarts.
The No 3 reactor at the Ikata nuclear plant in Ehime prefecture in the southwestern Shikoku region may come back online early next year, the Sankei Shimbun newspaper said.
The Asahi Shimbun meanwhile said the reactor at Ikata might resume operation in "the coming winter".
Anti-nuclear campaigner Greenpeace Japan said the country must seize the opportunity of being without nuclear power to focus on promoting renewable energy.