"The Federation will examine the details of the case and some form of punishment is expected," a spokesman told Reuters, adding that the football body was still awaiting all the details.
PAOK lost 1-0 to AEK Athens in a Greek Cup semi-final second leg match at Salonika's Toumba stadium that was marred by two outbreaks of violence.
The first came in the 58th minute when a flare hit AEK's Argentine goalkeeper Sebastian Saja. The player's jersey was singed but he was not injured.
A players' strike was narrowly averted last week after their PSAP union failed to get the backing of all 16 top flight clubs - a move prompted as a reaction to the increase in crowd violence.
Top clubs Olympiakos Pireaus and Panathinaikos were both handed supporter bans after hundreds of fans invaded the pitch, fighting police and attacking players following Olympiakos's 2-1 win over their closest rivals on February 19.
Panathinaikos assigned bodyguards to several players as the fall-out continued from what has been dubbed the "derby of shame" by Greek media.
