The Red Devils claimed a 1-0 away win over Ismaili on Saturday courtesy of a second-half strike from midfielder Mohamed Barakat.
But the match was disrupted by continuous crowd troubles from Ahli and Ismaili supporters.
Dozens of fireworks and seats were thrown onto the pitch as fans from both sides tried to unsettle the players.
Ahli players rushed into the tunnel right following the final whistle to avoid being hit by a barrage of seats thrown from Ismaili fans.
"There will be no room for leniency towards such behavior," Zaher told Al-Hayat TV after the game.
"The punishments we used at the past, like fines for example, will not take place anymore because they are useless.
"We will force the clubs of misbehaving fans to play outside their stadiums and without their supporters."
Zaher believes tough measures against rioters need to be taken sooner rather than later due to the country's international commitments in the upcoming period.
"We should crackdown on rioters quickly because Egypt have many important games in the World Cup qualifiers."
"Moreover, the country will host the U-20 World Cup later this year," he added.