Army vehicles surrounded entrances to the square outside the Rabaa al-Adawiya mosque in northern Cairo on Sunday, where Brotherhood supporters used pictures of the bearded Morsi to shelter from the fierce sun.
"We are right, legitimacy is on our side and hopefully at the end God will lead us to triumph and we will not give up," said Mostafa Ali, 29, from the Nile delta town of Mansoura.
The Interior Ministry has rejected eyewitness accounts that police opened fire on the crowds and a public prosecutor has launched a probe into the violence, investigating 72 suspects for an array of crimes including murder and blocking streets.
"They will not be content until they bring back everything from the era of the corrupt, murderous security and intelligence state," senior Brotherhood official Essam el-Erian said on Facebook. "They've stepped up their efforts to do so by committing massacres never before seen in Egyptian history."
Cairo was quiet on Sunday, but violent clashes rattled the Suez Canal city of Port Said, where a 17-year-old youth was killed in fighting between pro- and anti-Mursi camps and a further 29 people were injured, security sources said.
The violence has deeply polarized Egypt, with its secular and liberal elite so far showing little sympathy for the Brotherhood or reservations about the military's return to the political frontline.
In a first sign of doubt from within the interim cabinet installed after the military takeover, Deputy Prime Minister for Economic Affairs Ziad Bahaa El-Din said the government must not copy the "oppressive" policies of its foes.
"Our position must remain fixed on the need to provide legal guarantees not only for the members of the Brotherhood, but for every Egyptian citizen," Bahaa El-Din wrote on Facebook. "Excessive force is not permitted."
The Tamarud youth protest movement, which mobilized millions of people against Mursi and has fully backed the army, also expressed alarm at an announcement by Interior Minister Ibrahim that he was reviving Mubarak's hated secret political police, shut down after he was toppled.
Citing "extremist and religious activity and things like that," Ibrahim said on Saturday that "safety cannot be restored without political security".
The move, however, could shake the enthusiasm of some secularists, who have otherwise seen little to object to in a government campaign against their Brotherhood enemies.
'Can't rewrite history'
The military says it does not want to retain power and aims to hand over to full civilian rule with a "road map" to parliamentary elections in about six months. But the very public role of Sisi as face of the new order has sowed doubt.
The United States, which provides more than $1 billion a year in military aid to Egypt, urged its Middle East ally to pull "back from the brink" and respect the right to peaceful protest.
New York-based Human Rights Watch said the Saturday killings suggested a "shocking willingness" by police and politicians to ratchet up violence against backers of Mursi. U.N. human rights chief Navi Pillay said confrontation was "leading to disaster".
"Egypt stands at a crossroads," Pillay said in a statement. "The future of this great country that gave so much to civilization depends on how its citizens and authorities act over the following days and months."
Close to 300 people have died in violence since Sisi deposed Mursi.
Besides the Cairo bloodshed, some of the worst violence has been in the lawless Sinai peninsula, which borders Israel and the Palestinian Gaza Strip, where Islamist militants have targeted security forces on an almost daily basis.
State news agency MENA said on Sunday that 10 "terrorist elements" in north Sinai had been killed and 20 others arrested in security sweeps over the past 48 hours.
Egypt's Salafi Nour party, the country's second-biggest Islamist movement which has supported the army road map, said Saturday's bloodshed showed the need for a political solution.
"The crisis will not be resolved with crowds and counter crowds and neither will it be solved through violence," party chief Younes Makhyoun told Reuters.
Islamist politician and former presidential candidate Mohamed Selim al-Awa offered a compromise that would see Morsi reinstated but with new elections within months. It was swiftly rejected by the interim presidency and Egypt's biggest liberal and leftist coalition, the National Salvation Front (NSF).
"It's clearly a non-starter," said NSF spokesman Khaled Dawoud. "You can't rewrite history; Morsi is out and there is already a road map."