During Scotland’s goalless draw in the World Cup 2014 qualifier against Serbia earlier this month, Naismith was caught on camera elbowing Srdan Mijailovic.
Referee Jonas Eriksson and his officials missed the incident and therefore did not punish him at the time.
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However, Fifa regulation makes it possible for TV evidence to be used to help determine whether the striker is guilty of the offence and impose a suitable penalty.
Fifa confirmed that this particular case is being investigated by stating "We can confirm that Fifa has now opened disciplinary proceedings against the player Steven Naismith."
If Naismith is given a suspension he would miss the Group A games against Wales and Belgium, plus a friendly against Luxembourg.
Apart from suspending a player for three matches, the disciplinary committee can ban a player for two months and also impose a fine of up to £32,900.