Government officials say close to 600 people have been killed nationwide in the latest wave of violence.
With the country in a state of emergency and many provinces hit by night-time curfews, police have been ordered to use live fire if government buildings come under attack.
Hannah Sinclair reports.
Hundreds of people have been killed since Egypt's military-led government moved in to clear supporters of ousted President Mohamed Morsi from two protest camps in the capital, Cairo.
The death toll prompted the United Nations Security Council to call an emergency meeting in New York at the request of France, Britain and Australia.
Argentina's UN representative, Maria Cristina Perceval, says all members of the Security Council want to see the end of the violence in Egypt.
"The view of council members is that it's important to end violence in Egypt; that the parties exercise maximum restraint. And there was a common desire on the need to stop violence and to advance national reconciliation."
UN Secretary General Ban Ki-moon has condemned the Egyptian military's actions, and the UN's rights chief has urged a wide-ranging probe.
Foreign Minister Bob Carr says the most desirable outcome is if political prisoners are released and protesters return home.
Senator Carr told the ABC international condemnation of the Egyptian government is justified.
"The world community is entitled to assert to the government of Egypt, in a spirit of emphatic condemnation of the slaughter that has occurred, that we expect a political reconciliation to take place. And that involves the release of political prisoners and in return for that, demonstrators evacuating the streets and returning to their homes."
United States President Barack Obama also condemned the bloodshed and announced the cancellation of a joint US-Egyptian military exercise to be held next month.
But Mr Obama stopped short of suspending Washington's $1.3 billion in aid that it annually provides to Egypt.
"While we want to sustain our relationship with Egypt our traditional cooperation cannot continue as usual when civilians are being killed in the streets and rights are being rolled back. As a result, this morning we notified the Egyptian government that we're cancelling our biannual joint military exercise which was scheduled for next month."
The Obama administration has cautiously avoided describing the situation in Egypt as a military coup because U-S law says the country cannot provide aid to military-led governments.
Adel Abdel Ghafar is a PhD scholar at the Centre for Arab and Islamic Studies at the Australian National University.
Mr Ghafar says it's very unlikely that the Obama administration would cancel aid due to its significant relationship with the Egyptian government.
"The Egyptian-US strategic relationships is a cornerstone of peace in the Middle East. Cancelling of these military exercises is a slap on the wrist. But I do not see in the short term that the US will cancel any of the aid because its interests lie in giving aid to the Egyptian military."
In Cairo's Al-Iman mosque, dozens of corpses of protesters in white shrouds have been lined up.
While relatives seek to identify their dead, the Muslim Brotherhood has insisted that protesters will remain strong, defiant and resolved.
Brotherhood spokesman Gehad el-Haddad says despite this intention the movement has lost coordination and many protesters have turned violent.
"We're going to continue on the streets, peacefully protesting we refuse every type of violence. We are not affiliated with any type of instigated violence. Spontaneous reactions from the people after their loved ones have been killed or shot cannot be controlled. The military are the ones that are supposed to restrain itself. You can't ask the victim not to die, you're supposed to ask the killer not to kill. We will continue but we have lost central coordination so it's much more ad hoc at the moment and decentralised. It's a movement of the Egyptian people now."
The Coptic Orthodox community in Australia says Copts in Egypt are being used as scapegoats, caught between the army and pro-Morsi supporters.
They say dozens of churches and Christian schools have allegedly been burnt and destroyed during the clashes.
Leader of the Coptic Othodox Church in Australia, Bishop Suriel, says the attacks are unprecedented.
"People are dismayed and shocked and never expected this barbaric attack against our churches and of course the mayhem that has happened by the Morsi supporters. And we are saddened deeply by the great loss of life that has happened over the past couple of days."
A nationwide prayer vigil for the Australian Coptic community will be held tomorrow.
Adel Abdel Ghafar says the next few days in Egypt will most likely see more bloodshed.
Mr Ghafar says unless the Muslim Brotherhood negotiate there aren't many options available to the government.
"The Muslim Brotherhood will continue to push for more violence. The actual dispersement of the sit-in has been planned for about a month and half. It has been stopping traffic in key areas of Cairo. And they were actually expecting it and they refuse to come to the negotiating table. So I think the Muslim Brotherhood themselves, the current leadership, sees themselves as a generation of martyrs. They're actually just willing to die and not negotiate."
