London 2012 officials will try to establish if the flag mix-up before North Korea women's opening football match against Colombia was deliberate - as suggested by their coach.
They have apologised for the gaffe, which saw the South Korean flag being shown on the big screen at Hampden Park stadium as the players were warming up.
The North Koreans walked off in protest and the scheduled 7.45pm kick-off was delayed for more than an hour while officials tried to sort the matter out.
North Korea were eventually persuaded to return to the pitch when the sides were announced again and the correct flag displayed. They went on to win 2-0.
Coach Gun Sin Ui stressed the gravity of the incident and also revealed he planned to take up the matter with Games organisers Locog and Fifa, football's world governing body.
Ui said: "Our players were announced with their photos and names alongside the South Korean national flag. The national flag difference is a big problem.
"Our team was not going to participate unless the problem was solved properly. Unfortunately it took some time later for the broadcast to be done again properly and we made the decision to go on with the match."
Asked whether he believed the wrong flag had deliberately been used, Ui said: "That was the question I was going to ask Locog and Fifa.
"We were angry because our players were shown as if they were from South Korea which affects us very greatly.
"If this matter had not been solved, continuing would have been a nonsense."
A statement from the Games organisers said: "Today, ahead of the women's football match at Hampden Park, the South Korean flag was shown on a big screen video package instead of the North Korean flag.
"Clearly this is a mistake. We will apologise to the team and the National Olympic Committee, and steps will be taken to ensure this does not happen again."
South Korea and North Korea exist as neighbours, but have a far from harmonious relationship. The countries were formally established as separate entities in 1948, when US forces occupied the south and Soviet forces occupied the north.
The north established itself as a communist state, tensions escalated and the Korean War began in 1950.
The US was among those countries to fight against North Korea. Some 100,000 British troops saw action and the conflict is often called Britain's "forgotten war".
Only two years ago, North Korean artillery shells killed four people, two from the military and two civilians, on Yeonpyeong Island in South Korea.
Technically, the two countries are still at war and Pyongyang has yet to officially respond to the flag gaffe.