The man, identified only by his surname Choi, allegedly climbed over the wall of the embassy Friday evening after Japan claimed sovereignty over South Korea's easternmost islets of Dokdo earlier in the day, Yonhap news agency reported.
Choi has a history of carrying out anti-Japanese protests, Yonhap said.
He allegedly threw a bottle of human feces into the embassy in August, in anger over Japan's sovereignty claims to the East Sea islets. He allegedly cut off part of his little finger and mailed it to the embassy for the same reason in 2010.
Japan's Shimane prefecture Friday held its annual "Takeshima Day" event, Japan's name for the islets. The event is aimed at reinforcing Japan's claims over Dokdo.
South Korea, which has rejected Japan's claims to Dokdo, filed a protest, calling Japan's claims "unjustifiable."