State television quoted the Health Ministry as saying Thursday that five people were killed and 644 injured by beatings, gunshot wounds and tear gas inhalation.
Morsi, meanwhile, seemed determined to press forward with plans for a Dec. 15 constitutional referendum to pass the new charter. The opposition, for its part, is refusing dialogue unless Morsi rescinds the decrees giving him near unrestricted powers and shelves the controversial draft constitution, which the president's Islamist allies rushed through last week in a marathon, all-night session shown live on state TV.
Mohamed ElBaradei, a leading opposition reform advocate, said late Wednesday that Morsi's rule was "no different" than Mubarak's.
"In fact, it is perhaps even worse," the Nobel Peace Prize laureate told a news conference after he accused the president's supporters of a "vicious and deliberate" attack on peaceful demonstrators outside the palace.
"Cancel the constitutional declarations, postpone the referendum, stop the bloodshed, and enter a direct dialogue with the national forces," he wrote on his Twitter account, addressing Morsi.
Wednesday's violence spread to other parts of the country. Anti-Morsi protesters stormed and set ablaze the Brotherhood offices in Suez and Ismailia, east of Cairo, and clashes broke out in the industrial city of Mahallah and the province of Menoufiyah in the Nile Delta north of the capital.
Rival demonstrations also were held outside the Brotherhood's headquarters in the Cairo suburb of Moqatam and security officials said senior Brotherhood official Sobhi Saleh was hospitalized in Alexandria after being severely beaten by Morsi opponents. Saleh, a former lawmaker, played a key role in drafting the disputed constitution. The officials spoke on condition of anonymity because they were not authorized to speak to the media.