With hundreds of thousands taking to the streets on Friday, the new bloodshed deepened the turmoil convulsing the Arab world's most populous country, and could trigger a decisive move by the military against Morsi's Muslim Brotherhood.
At least seventeen people have been killed so far while several hundred were hurt in confrontations nationwide.
In Cairo, the pro-Morsi camp said one Brotherhood supporter had been killed when "thugs" opened fire with tear gas and rubber bullets.
Egypt's army-installed interior minister, Mohamed Ibrahim, said month-old Cairo vigils by supporters of the deposed leader would be "brought to an end, soon and in a legal manner," state-run al Ahram news website reported.
In the sprawling capital, huge crowds heeded a call by army chief General Abdel Fattah al-Sisi to give him a popular mandate to confront violence unleashed by his July 3 overthrow of Morsi, who remains in military detention.
Following Sisi's call, news of the investigation against Morsi over a 2011 jailbreak signaled an escalation in the military's confrontation with the Brotherhood.
The Brotherhood fears a broad crackdown to wipe out a movement that emerged from decades in the shadows to take power after Egypt's 2011 Arab Spring uprising against autocrat Hosni Mubarak, only to be deposed a year later by the powerful military.
In Egypt's second largest city Alexandria, on the Mediterranean coast, hundreds of people fought pitched battles, with birdshot fired and men on rooftops throwing stones at crowds below.
Seven people were killed in fresh clashes in Alexandria.
Dozens of people have died and hundreds more have been injured in deadly clashes between Morsi supporters and security forces over the last two weeks.
On July 3, the head of Egypt’s army chief al-Sisi announced that president Mohamed Morsi was no longer in power. Al-Sisi also dissolved the Egyptian constitution.
The Chief Justice of Egypt’s Supreme Constitutional Court, Adli Mansour, was sworn in as interim president on July 4.
Since then, Egypt has been the scene of rival rallies and clashes between thousands of the supporters and opponents of Morsi.
NTJ/SHI