This is the first such attempt on a commercial unit in Japan, after Chubu Electric decided in 2008 to dismantle two reactors at its Hamaoka plant in the central Shizuoka region, to avoid paying for costly anti-earthquake measures for them.
Only about 25 nuclear reactors worldwide have been fully dismantled, according to the World Nuclear Association.
Japan, targeting net-zero emissions by 2050, is shifting back to nuclear power after shutting down all its 54 reactors after the tsunami-triggered 2011 Fukushima meltdown.
Under its current plan, Japan aims for nuclear power to account for 20-22 percent of its electricity by 2030, up from well under 10 percent now.
It is slowly bringing its still-operable units online, and also plans to extend their lifespan, while encouraging the development of next-generation atomic plants.
On Monday, Chubu Electric began removing the top lid of its "Number Two" reactor at Hamaoka, before a similar exercise starts for another unit at the same plant, a company spokesman told AFP Tuesday.
The complicated dismantling process is expected to continue until 2042, which means building a replacement reactor is still many years away.
A total of 26 reactors in Japan, including the Hamaoka units and research units, are currently slated for dismantling, according to the Nuclear Regulation Authority.
Japan scrapped a research reactor in the 1990s after it ended operations in 1976.
Meanwhile Japan is also embroiled in a decades-long project to scrap the damaged reactors at Fukushima Daiichi plant, which was hit by a huge tsunami in 2011, triggering the world's worst nuclear disaster since Chernobyl.
hih/kaf/sn
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