Zamalek supporters, following in the footsteps of Ahly's fans, defied a crowd ban during Sunday's 2-1 Egyptian Premier League win over Ismaily on Sunday.
Crowds have been barred from attending domestic football games since February 2012, when post-match violence between Ahly and Masry fans left more than 70 dead.
"We let around 3,000 Zamalek fans enter the stadium," Khaled Metwally, an interior ministry official, said in a television interview.
"Our mission is to secure the stadium and the fans and not to apply the orders of the Egyptian football association."
Some of the supporters of Ittihad of Alexandria have also sneaked in to attend their side's game against Arab Contractors.
The Egyptian football Association (EFA) stated last Thursday that a game would be called off if the supporters of either side violated the crowd ban. It also said the visiting them would be awarded a 2-0 walkout win.
However, Ahly's die-hard supporters (Ultras Ahlawy) briefly stormed the Air Defence Stadium in Cairo in their side's 4-1 Egyptian Premier League win over Gouna on Saturday. They left the venue after 10 minutes and the match went ahead as scheduled.
The EFA will convene in the next few days to decide which action it would take in the wake of the mass stadium invasions.
Zamalek's game against Ismaily was largely meaningless, given that both sides had already secured their place in the final four-team phase of the league's new format.
Midfielder Ahmed Khairy gave Ismaily the lead after 27 minutes with a header but Mohamed Ibrahim restored parity after converting a 33rd-minute penalty.
Veteran midfielder and former Egypt skipper Ahmed Hassan gave Zamalek all three points with a 59th-minute strike.
Group B leaders Zamalek and runners-up Ismaily will compete with Ahly and ENPPI in a mini-league phase with only home fixtures to determine the league champion.
The last round should start at the end of the month but is likely to be postponed by the EFA, given planned protests against Egyptian President Mohamed Morsi's rule on 30 June.
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