"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.
Then, with barely a minute remaining, dozens of PAOK fans invaded the pitch and started clashing with riot police. TV cameras were also attacked as AEK players and the referee ran off the pitch.
Play was suspended for 20 minutes before the referee returned to blow the final whistle. No stoppage time was played.
The incident was the fifth pitch invasion of a season plagued by violence inside and outside Greek stadiums.
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.
Attacks by supporters on the Super League offices and the home of Olympiakos player Vasilis Torosidis followed.
Panathinaikos assigned bodyguards to several players as the fall-out continued from what has been dubbed the "derby of shame" by Greek media.
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