Two people have died in clashes between police and supporters of the Muslim Brotherhood in the Suez Canal city of Ismailia, a medical source told Ahram Online.
Another protester was also killed in the governorate of Fayoum in southern Egypt, a health ministry official in the city told Ahram Online.
Scores of others were injured as supporters of the Islamist movement clashed with security forces in Cairo and elsewhere.
The group's supporters have continued protests although the government designated the Brotherhood a terrorist organisation last month.
Eyewitnesses told Al-Ahram's Arabic website that protesters in the Giza's Faysal district threw Molotov cocktails at an armoured police vehicle, setting it on fire, and shot at police officers trying to escape from the car.
A pro-Morsi grouping led by the Brotherhood had called for Friday demos in the run-up to their planned boycott of the upcoming constitutional referendum.
Supporters of Morsi reject the new constitution, which was amended after Morsi's ouster.
Recent months have seen regular clashes between protesters and security forces during weekly Friday protests.
Later in the day, police fired teargas when some 300 pro-Brotherhood protesters blocked off Cairo's corniche road near the High Administrative Court in the southern suburb of Maadi. Protesters responded with stone-throwing.
Egypt's authorities declared the Brotherhood a terrorist organisation in December, accusing the group of links with recent attacks on state institutions and on churches since Morsi's ouster.
Ministry of Interior officials have warned that anyone taking part in pro-Brotherhood protests after its designation as a terrorist organisation will be punished with five years in jail, while protest leaders might face the death penalty.
Clashes also erupted in the northeastern district of Nasr City. Protesters threw rocks and fireworks at police and set tyres on fire. Security forces fired teargas to scatter the crowds, Al-Ahram added.
A public bus was smashed and several cars were shattered in the violence.
Police fired teargas at a student march at the nearby Al-Azhar University, a major scene of Islamist protest in recent weeks, state news agency MENA said.
Security forces have closed off Cairo’s Tahrir Square, as well as Rabaa Al-Adawiya and Nahda Squares, sites of major pro-Morsi protests over the summer, ahead of the demos.
Violence also flared in Egypt's second city of Alexandria when hundreds of Islamists clashed with civilian opponents, using stones and birdshot. Security forces stepped in to scatter the crowds, arresting several pro-Brotherhood protesters in possession of "rioting tools" and leaflets against the police and army.
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