Morsi's Muslim Brotherhood movement called for more protests, raising the risk of further violence, although an umbrella group representing anti-Morsi protesters said they would not demonstrate.
The bloodshed has shocked Egyptians, already tired of the turbulence that began two and a half years ago with the overthrow of autocrat Hosni Mubarak.
It also raised alarm among key donors like the United States and the European Union, as well as in Israel, with whom Egypt has had a US-backed peace treaty since 1979.
Millions of people took to the streets on June 30 to demand Morsi's resignation, fearing he was orchestrating an Islamist takeover of the state - a charge the Brotherhood has denied.
But for many Islamists, the overthrow of Egypt's first freely elected president was a bitter reversal that raised fears of a return to the suppression they endured for decades under rulers like Mubarak.
The Brotherhood movement has refused to have anything to do with the process, and thousands of supporters have camped out in northeast Cairo for the last five days and vowed not to budge until Morsi returns as president.
The United Nations said it was gravely concerned about mounting violence in Egypt and said the country was on a precarious path.
The United States called on Egypt's army to exercise "maximum restraint". The White House said it was not about to halt aid to Egypt.
The Egyptian military, recipient of US$1.3 billion ($1.6 billion) a year from Washington, has insisted the overthrow was not a coup and that it was enforcing the "will of the people".
Tentative steps to democracy
Is the violence limited to Cairo?
No. While dozens have been killed in the capital, the unrest has occurred throughout the country. Instability has spread and grown since the Egyptian military intervened to throw out the Islamist government. Attacks have included the murder of a Coptic priest in Sinai and the deaths of two men, who were allegedly thrown from a roof by members of a pro-Morsi mob in Alexandria.
How does the Muslim Brotherhood plan to withstand the assault on its power?
After a year in control of the presidency, the Muslim Brotherhood is back in familiar territory as it challenges the military from the street. The Muslim Brotherhood is not backing down. The leadership has called for an uprising, though it is not clear what form this will take. At a minimum there will be a cycle of daily protests, centred around demonstrations after daily prayers.
Q: How does the Egyptian army hope to manage the transition?
The options are narrowing for the generals. The military had hoped to follow a "roadmap" by drawing on judges, technocrats and some non-Muslim Brotherhood politicians to run the country until elections under a new constitution. It is clear that Gen Abdel-Fatah al-Sissi is in charge and the interim president, Adly Mansour, is a figurehead.
How has the international community reacted to events in Egypt?
There has been a low-key and awkward international response to the collapse of the first democratically elected Egyptian government. Western governments had a tacit policy of supporting the rise of the Muslim Brotherhood to power through the ballot box. By now Egypt should have been a post-Arab Spring showcase with the military subordinated to civilian control.
