Morsi's party, the Muslim Brotherhood, said 213 people had died across the country, including more than 100 in central Cairo alone, The Washington Post reported. The Egyptian Health Ministry said only 27 had died, The New York Times reported.
Friday's carnage followed more than 600 deaths Wednesday when security forces cleared two sit-ins in Cairo.
The Muslim Brotherhood called for more marches Saturday. Demonstrations began after the military deposed Morsi July 3 and installed an interim government.
The satellite broadcaster al-Jazeera reported Turkey condemned the Egyptian government actions while gulf states expressed support. Turkey and Egypt recalled their respective ambassadors and RT reported the countries canceled planned joint naval maneuvers.
The BBC reported 12 bodies outside a mosque in Ramses Square and gunfire on the banks of the Nile. Armored personnel carriers patrolled the streets as Tahrir Square, where protesters staged the demonstrations that toppled Hosni Mubarak in 2011, was blocked off.
The Muslim Brotherhood adopted the slogan "the people want to topple the coup" for their protests as the National Salvation Front and Tamarod called for counter-demonstrations in support of the interim government.
The British newspaper The Daily Telegraph reported on Twitter snipers were firing on the protesters. There also were reports of security forces firing at protesters from helicopters.
Demonstrators stormed across the May 15 Bridge into central Cairo as authorities blocked the Oct. 6 Bridge. RT reported tear gas canisters were lobbed into the crowds in Ramses Square as protesters threw stones and fireworks. Smoke could be seen billowing over the square.
ChannelNewsAsia reported people jumped off bridges to avoid gunfire.
RT reported the railroad north of Cairo that connects Alexandria and Marsa Matrouh was damaged by a bomb.
Friday's rallies following early afternoon congregational prayer were meant to vent Islamists' anger over the regime's bloody crackdown, the Muslim Brotherhood said.
They also challenged the government's monthlong nationwide state of emergency and a dusk-to-dawn curfew, said the Islamist religious, political and social movement.
Egypt's civilian Cabinet said the state of emergency imposed Wednesday, which gives security services sweeping powers, was only a "temporary procedure forced by circumstances." It promised some restrictions would be eased soon.
The state of emergency imposed by Mubarak in 1981 lasted until after his Feb. 11, 2011, overthrow.
The Health Ministry said Thursday 638 civilians were killed nationwide in Wednesday's clashes, including nearly 300 at one of the two Cairo sit-ins by Morsi backers.
More than 4,200 people were injured, the ministry said.
A ministry official told the Post the death toll could actually be as high as 700 while the Muslim Brotherhood put the death toll at 2,600 and the number of injured at 10,000.
Even with the lower death count, Wednesday's casualties marked the bloodiest single day since Egyptians rose up against Mubarak's three-decade rule 31 months ago.
Egypt's Interior Ministry said, as part of emergency rule, it gave its troops in Cairo and elsewhere an order to use lethal force when necessary.
"The ministry has given instructions to all forces to use live ammunition in the face of any attacks on establishments or forces within the framework of the regulations of using the legitimate right of self-defense," the ministry said in a statement, defying calls for restraint from Washington and European capitals.
The military-led regime of interim President Adly Mansour also said U.S. President Barack Obama -- who interrupted a weeklong vacation to condemn the bloodshed -- failed to grasp the nature of the "terrorist acts" it said Egypt faced.
Obama's remarks will "strengthen the violent armed groups and encourage them in their methods inimical to stability and the democratic transition," a statement from Mansour's office said.
Obama in his remarks did not suspend the $1.3 billion in annual U.S. military aid to Egypt but canceled joint military exercises scheduled to take place next month and ordered his national security team to consider "further steps that we may take as necessary."
Shortly after Obama's remarks, the State Department warned U.S. citizens living in Egypt to leave "because of the continuing political and social unrest."