Masao Jitsui, 40, of Miki, Hyogo prefecture was charged with a misdemeanor count after being taken into custody shortly before 10 p.m. local time.
Jitsui allegedly told police he was "not satisfied that South Korea repatriated to China an arsonist responsible for an attack at the Yasukuni Shrine," Kyodo News reported.
Jitsui apparently was referring to a South Korean court decision Thursday against extraditing to Japan a Chinese man who allegedly set fire to a gate of the shrine dedicated to the war dead.
No one was injured in the incident, Kyodo said.
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