"Japan must well be aware that the Rising Sun Flag is perceived by many of its neighboring nations as the symbol of its past militarism and imperialism", ministerial spokesman Kim In-chul was quoted as saying by South Korea's Yonhap news agency.
He told reporters at a press briefing that the South Korean government would work with the relevant ministries to "correct the matter".
The Japanese Olympic Committee has reportedly refused to ban spectators from displaying the flag in any form despite it being associated with Japanese militarism in South Korea and China.
Japan adopted a new official flag in 1999 that features a red sun disk. The nation's navy, however, still uses the flag depicting the rising sun, the war flag of imperial Japan's navy and army since the 19th century and until its WWII defeat in 1945. In Korea, it is associated with the Japanese colonial rule.