"Our match officials are not small individuals [to take sides]," Masuod Enayat, the head of the IFF Referee Committee said on Friday.
The allegations of referees' siding with Esteqlal climaxed after the match official ruled out Persepolis' first-half onside goal as offside in the Tehran derby last Friday.
Persepolis ended up losing the match 1-0 in injury time.
"What they say that in the derby the referee was biased towards Esteqlal because [Persepolis manager] Ali Daei had earlier filed a complaint with the IFF is a disgrace to the referee society," Enayat was quoted by IRNA as saying.
He went on to add that Iranian referees are among the best in Asia. "Should any of the 11 match officials elected by the Asia Football Confederation (AFC) for the Asian championship fail the physical fitness test, Iranian Mohsen Torki will be the first to take their place."
Enayat's remarks came after Esteqlal managed to capitalize on refereeing mistakes to avoid defeat or marginally win the matches on a number of occasions this season.