The governing body has moved swiftly to stop one of the winners, who held aloft a sign displaying a political message, from receiving his prize
After being photographed holding aloft a sign sporting a political message in the aftermath of South Korea's 2-0 victory over Japan at the Millennium Stadium in Cardiff on Friday, Jong-Woo Park was blacklisted.
The 23-year-old, who plays for K-League side Busan IPark, did not feature at the medal ceremony after the culmination of the men's final at Wembley Stadium on Saturday as only 17 squad members received medals.
The sizeable card read "Dokdo is our territory" according to Reuters, which refers to the islands which are at the centre of a territorial dispute between the two countries.
Tensions between South Korea and Japan have soured in recent days, with the Japanese ambassador being recalled from Seoul.
The IOC announced in a statement: "We have opened an inquiry and have asked the NOC (National Olympic Committee) of the Republic of Korea for an explanation. We have also requested that the Republic of Korea NOC takes swift action on this issue and that the athlete not be present at this afternoon's medal presentation ceremony."
South Korea's chief of staff at London 2012 has meanwhile insisted that the country will take the matter seriously.
"We just heard about what happened yesterday, we are looking into this incident but we are taking it very seriously," John Moon was quoted as saying.
"According to the IOC rules politics has no place in sport."