At least 10 people were also injured in the violence in Cairo's Giza neighborhood on Tuesday, said security officials.
A pro-Morsi march had taken off from Nahda square -- site of one of two large sit-ins staged by Morsi loyalists -- to Faisal Street in Giza where residents began to pelt the marchers with rocks.
The clashes rapidly escalated with birdshot fired from both sides, security officials said, as residents of the Giza neighborhood smashed the shopfront of a department store owned by pro-Morsi Egyptians.
Earlier in another area of the capital, police fired tear gas to break up clashes that erupted between Morsi loyalists and residents, AFP correspondents reported.
Dozens of religious scholars affiliated with Morsi's Muslim Brotherhood had entered the religious endowments ministry and were ordered out by police prompting clashes, a security official said.
The violence comes after the expiry of a government ultimatum to dismantle the sprawling protest camps.
Morsi, Egypt's first elected president, was overthrown by the military on July 3 with popular backing.
His supporters say nothing short of his reinstatement will persuade them to disperse.
The standoff with the army-backed interim government has sparked international fears of further bloodshed.
Clashes between pro- and anti-Morsi demonstrators and security forces have killed more than 250 people since the end of June.
BA/BA