The Egyptian government has declared a month-long state of emergency following the 14 August crackdown on the pro-Mursi protest camps in Cairo.
Curfews are now in place in the countrys cities.
The violent clearing of the sit-ins held at the Nahda and Rabaa al-Adawiya squares saw hundreds of people killed, including Muslim Brotherhood supporters, members of the security forces and three journalists.
The number killed in the clashes is disputed. The Health Ministry sets the current death toll at 421, while the Brotherhood says more than 2,000 were killed.
According to the organisation, protesters tents sheltering women and children were burnt down and demonstrators were targeted by snipers.
However, the group said it would continue its protest against the incumbent government. The [anti-coup] reiterates its call to all Egyptians to [join] in non-violent vigils and protest rallies in public squares in all the provinces of Egypt, until the coup is completely defeated, said the organisation in a statement.
The Brotherhood wants to see the reinstatement of former president Mohamed Mursi, who was overthrown by the military on 3 July.
The use of violence to clear the camps has been widely condemned by global powers. The White House issued a statement saying the US strongly condemns the use of violence against protesters and opposes the return to a state of emergency law. Todays events are deplorable and they run counter to Egyptian aspirations for peace, inclusion and genuine democracy, said US secretary of state John Kerry.
The EU has condemned the carnage in Cairo. EU high representative Catherine Ashton said: Confrontation and violence is not the way forward to resolve key political issues. The UN secretary-general Ban Ki-Moon spoke out against the use of violent tactics.
The ruling Islamist Ennahda party in Tunisia has criticised the Egyptian armys violent tactics, with party leader Rached Ghannouchi referring to the crackdown as a massacre.
In contrast, the UAE Ministry of Foreign Affairs issued a statement saying it reaffirmed its understanding of the sovereign measures taken by the Egyptian government after having exercised maximum self-control.
What is regretful is that political extremist groups have insisted on the rhetoric of violence, incitement, disruption of public interests and undermining of the Egyptian economy, which has led to the regretful events today, the ministry stated.
Bahrains government called for a national reconciliation in Egypt, but added that measures by the relevant authorities to restore security, peace and order to public life are the right of Egyptian citizens guaranteed by the state.
Egypts interim Prime Minister, Hazem Beblawi said in a televised address that the military action was a necessary means of restoring security to the country, although he expressed regret at the deaths.
Egypts government says the Muslim Brotherhood were armed and firing at the security forces. There are reports that the organisation has burnt down churches and other buildings in retaliation to the militarys action.
However, interim Vice-president Mohamed el-Baradei has resigned from his position, saying: It has become difficult for me to continue bearing responsibility for decisions that I do not agree with and whose consequences I fear. I cannot bear the responsibility for one drop of blood.
During the weeks of sit-ins, there were numerous attempts by Western and Arab powers to broker a compromise between the Muslim Brotherhood and the government.
In the aftermath of the violence seen on 14 August, reaching a form of compromise is set to be far harder.
Security operations have likely dashed any hope of understanding/negotiations between the army-backed government and the Brotherhood in the near term, says Raza Agha, chief economist for the Middle East and Africa at UK-based VTB Capital. Our worry is that given the public and political support the incumbent regime had in ousting the Mursi administration, todays actions have taken ideological divisions in Egypts political fabric to a significantly worse level.