South Korea lost to Japan ten-to-eight on Saturday at the last Super Round game of the Premier 12 baseball tournament in Tokyo.
Controversy emerged, as some Japanese fans in the stadium were spotted with the Rising Sun Flag, which is considered a symbol of Japan's wartime aggression.
The Korea Baseball Organization raised the issue with the World Baseball Softball Confederation.
The match on Saturday was little more than an exhibition for both sides, with South Korea already securing its Olympic berth on Friday, and Japan automatically qualifying as the host country.
The two rivals will clash again in the Premier 12 championship final at 7PM later tonight.