The street battles outside the presidential palace in the city's Heliopolis district were the worst violence since Egypt's latest political turmoil erupted on Nov. 22, when Morsi assumed near absolute powers.
It was also the first time supporters of rival camps have fought each other since last year's uprising that toppled authoritarian ruler Hosni Mubarak.
A statement from the ministry early Thursday said there were also 276 people injured in the clashes, including 35 policemen, as angry mobs battled each other with firebombs, rocks and sticks outside the presidential complex.
The fighting erupted late Wednesday afternoon when thousands of Morsi's Islamist supporters descended on an area near the presidential palace where some 300 of his opponents were staging a sit-in. The Islamists, members of Morsi's Muslim Brotherhood, chased the protesters away from their base outside the palace's main gate and tore down their tents.
After a brief lull, hundreds of Morsi opponents arrived and began throwing firebombs at the president's backers, who responded with rocks. The clashes continued well after nightfall and spread from the immediate vicinity of the palace to residential streets nearby.
The deployment of hundreds of riot police did not stop the fighting. The police later fired tear gas to disperse Morsi's opponents. Volunteers ferried the wounded on motorcycles to waiting ambulances, which rushed them to hospitals.
By dawn, the violence had calmed. But both sides appeared to be digging in for a long struggle, with the opposition vowing more protests later Thursday and rejecting any dialogue unless the charter is rescinded.
Morsi, for his part, seemed to be pressing relentlessly forward with plans for a Dec. 15 constitutional referendum to pass the new constitution.
The large scale and intensity of the fighting marked a milestone in Egypt's rapidly entrenched schism, pitting the Brotherhood and ultra-conservative Islamists in one camp, against liberals, leftists and Christians in the other.
The violence spread to other parts of the country on Wednesday. Anti-Morsi protesters stormed and set ablaze the Brotherhood offices in Suez and Ismailia, east of Cairo, and there were clashes in the industrial city of Mahallah and the province of Menoufiyah in the Nile Delta north of the capital.
Compounding Morsi's woes, four of his advisers resigned Wednesday, joining two other members of his 17-member advisory panel who have abandoned him since the crisis began.