Four firebombs were tossed at the Japanese Embassy in Seoul on Sunday by a Chinese man who said his grandmother was a sex slave of the Imperial Japanese military during the war.
There was no immediate report of injuries, and police subdued the man on the spot.
The man, 37, reportedly said he was angry about "irresponsible remarks" Prime Minister Yoshihiko Noda made on the sex slave issue. The women who were involved are euphemistically called "comfort women" in Japan.
South Korean Foreign Minister Kim Sung Hwan told Japanese Ambassador Masatoshi Muto through his deputy that the incident was regrettable, the Japanese Embassy said. Muto asked Kim to investigate the incident and prevent a similar one from ever happening again, it added.
South Korean police may seek a warrant to arrest the man for violating a special law on firebombs, they said.
According to the police, the man claimed that he ignited the gate to Yasukuni Shrine in Tokyo on Dec. 26. The Shinto shrine served as the spiritual backbone for Japan's war of aggression.
A guard at the shrine found a burn mark on the gate to the shrine at around 4:10 a.m. that day, and a man who looked like he was trying to start a fire there was spotted in video footage from a security camera.
South Korean police confirmed that the man, who hails from Guangzhou and claims to be a doctor specializing in treating psychological disorders, entered South Korea via Japan on Dec. 26 on a tourist visa after taking part in volunteer activities for two months in disaster-hit Fukushima Prefecture.
The man had prepared 11 firebombs, they said.