National flags of the 45 countries participating in the games had flown in streets of Incheon and nine nearby cities since last Friday. But they were replaced by flags of the Olympic Council of Asia and flags bearing the games' emblem following complaints about the flying of North Korea's colours, according to the games' organizing committee.
Relations between the Koreas remain strained with North Korea conducting a slew of rocket and missile test-launches and South Korea rejecting the North's calls for improving ties, citing the lack of sincerity.
North Korea is sending a 273-member delegation to the games, which includes athletes, coaches and judges, with 94 of them due to fly to South Korea from Pyongyang later Thursday. The North has cancelled its previous plans to dispatch cheerleaders in protest at what it calls Seoul's hostility.
North Korea boycotted the 1986 Asian Games and the 1988 Summer Olympics, both in Seoul, but has since attended several other major sports events held in the South.
North Korean flags were hoisted along with other countries' flags on South Korean streets during the 2002 Asian Games in Busan and the 2003 University Games in Daegu when South Korea was ruled by liberal governments supporting greater reconciliation with North Korea.
The Korean Peninsula is divided along the world's most heavily fortified border and remains in a technical state of war since the 1950-53 Korean War ended with an armistice, not a peace treaty.