At least 10 people were injured in the violence in Cairo's Giza neighbourhood on Tuesday, security officials said.
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 neighbourhood smashed the shop-front of a department store owned by Islamists.
Earlier in another area of the capital, police fired tear gas to break up clashes that erupted between Morsi loyalists and residents.
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. Since police issued the latest warning last week to end the protests, the Islamists have repeatedly called for new demonstrations.
On Monday, the judiciary extended Morsi's detention for a further 15 days pending an investigation into his collaboration with Palestinian group Hamas.
Morsi's backers set as their rallying cry, "Together against the coup d'etat and the Zionists", in an appeal to nationalist sentiment after a deadly air strike on militants in Egypt's Sinai Peninsula, which the jihadists said was carried out by an Israeli drone.
Israeli media say the Jewish state has been cooperating closely with Egypt over the threat from Sinai militants. Authorities have announced plans to clear the pro-Morsi protest camps from Cairo's Rabaa al-Adawiya and Nahda squares by "gradual steps". But the number of protesters in the squares has not diminished.
At Rabaa, the bigger of the two rallies, dozens of volunteer guards manned makeshift barriers of bricks and sandbags.


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