At least 1,000 people were injured in the clashes -- 150 of them critically -- spokesman Dr. Hisham Shiha said. Most of them had concussions and deep cuts, he said.
The fighting occurred in a stadium in the northeastern city of Port Said after Port Said's Al-Masry team beat Cairo's Al-Ahly team 3-1.
Fans from both sides bashed each other with rocks and chairs, said Mohamed Sultan, head of the ambulance association in Port Said.
Rescuers treated 60 people on the ground, he said, and dozens of ambulances were at the stadium.
Authorities have been dispatched to hospitals to interview the wounded and investigate what caused the clashes, said Adel Saeed, a spokesman for Egypt's general prosecutor.
Egypt's military deployed two planes to transport the Al-Ahly team, some of its fans and some of the injured back to Cairo, he said.
While authorities were responding to the fighting in Port Said, a fire broke out during a match in Cairo stadium. It was not immediately clear if the incidents were related.
"It's not unheard of to have organized violence between football clubs (in Egypt), but something on this scale has never been seen before," said James Montague, a CNN contributor who researched soccer in the Middle East for his book "When Friday Comes: Football in the War Zone."
During Egypt's revolution, well-organized groups of soccer fans became a powerful force for political change, he said. Soccer was also closely tied with former Egyptian President Hosni Mubarak's government, who used the sport to boost his popularity, Montague said.
But it was unclear whether political fury fueled Wednesday's clashes.
"There's been a security vacuum, so we don't know whether it's that or whether there's a Mubarak element to it. We just don't know at the moment," Montague said.
