Molotov cocktails, rocks and bricks were thrown during clashes with military and security forces outside Parliament, where activists have been camped for weeks protesting the military-appointed prime minister, CNN reported.
Military officials said warning shots were fired and water cannons sprayed to try to disperse the crowd.
Activist and video blogger Walid Nada told CNN the violence started when the military arrested an activist. He was later found badly beaten, witnesses said.
A spokesman for the Ministry of Health said nearly 100 people were hurt, including nine who suffered gunshot wounds.
CNN said men wearing what appeared to be military uniforms were seen tossing bricks and cement on protesters from a six-story building.
A Ministry of Interior official denied police were involved in the violence.
The violence broke out as election judges reported the moderate Muslim Brotherhood's Freedom and Justice Party appears to have led Wednesday's parliamentary elections, followed by the ultraconservative Salafis and an alliance of liberal and leftist parties known as the Egyptian Bloc, The New York Times reported.
The Muslim Brotherhood said voter turnout for the second phase of Egypt's three-part election process was estimated at more than 30 percent. The group alleged some election judges were urging people to vote against the FJP, the Egyptian news Web site al-Masry al-Youm reported.
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