The reactor at the Tomari atomic power plant in Hokkaido shuts down about 13 months after the Fukushima nuclear plant disaster, The Washington Post reported.
While the central government says it's committed to nuclear power, local communities and provincial governors express doubts that nuclear power is needed or that the nuclear regulatory agency can ensure safety.
Nuclear decisions in the country are made based on local consensus, the Post said, and regular maintenance checkups, required every 13 months, have led to indefinite shutdowns.
Before the Fukushima plant was heavily damaged in last year's earthquake and tsunami, 54 commercial nuclear reactors were operating in Japan and they provided about a third of the country's energy supply.
But 17 of those reactors were damaged in the earthquake-tsunami or shut down at the request of the government Thirty-six taken off-line for inspections haven't been restarted.
Critics complain the Japanese government hasn't done enough to improve nuclear safety standards and point to close relationships between the government and the nuclear industry.
The lack of nuclear power has led to concerns about a summer energy shortage and experts said it could be months before a new nuclear safety agency is created.