last month of President Mohamed Morsi, the country's new rulers have upped the rhetoric, saying the Arab world's most populous nation is at war with terrorism.
More than 700 people have died, most of them backers of Morsi, in four days of violence. That has earned Egypt stiff condemnation from Western nations, uncomfortable with Islamist rule, but also with the overthrow of an elected government.
The crackdown has, however, drawn messages of support from key Arab allies like Saudi Arabia, which have long feared the spread of Brotherhood ideology to the Gulf monarchies.
Blaming a defiant Brotherhood for the bloodshed, Egyptian Prime Minister Hazem el-Beblawi proposed dissolving the group in a move that would force it underground and could usher in mass arrests of its members countrywide.
The government said it was studying the possibility. "There will be no reconciliation with those whose hands have been stained with blood and who turned weapons against the state and its institutions," Beblawi told reporters.
Violence flared briefly on Saturday as Morsi's supporters exchanged fire with security forces in a central Cairo mosque, where scores of Muslim Brotherhood protesters had sought refuge from clashes the day before that killed 95 in the capital.
Police finally cleared the building and made a string of arrests, with crowds on the street cheering them on and harassing foreign reporters trying to cover
"We as Egyptians feel deep bitterness towards coverage of the events in Egypt," presidential political advisor Mostafa Hegazy said, accusing Western media of ignoring attacks on police and the destruction of churches blamed on Islamists.
Founded in 1928, the Brotherhood has deep roots in the provinces and won all five elections that followed the overthrow in 2011 of the autocratic Hosni Mubarak, appearing to cement themselves in the heart of Egyptian power for years to come.
But accusations that they were incompetent rulers intent only on monopolising government tarnished their reputation.
Hundreds of thousands of Egyptians took to the streets in June to denounce Morsi and the army says it removed him from office on July 3 to avoid a civil war.
Since then, the state media has turned ferociously against the group and there appeared to be little sympathy for the Brotherhood faithful amongst many ordinary Egyptians.
"Democracy did not work for Egypt I am afraid," said Hussein Ahmed, a 30-year-old Egyptian banker in Cairo, who had protested against Mubarak in the 2011 uprising.
"Yes the Brotherhood were elected, but they never cared about rights or freedoms of anyone but their own group. Why should we feel sorry for them now?"
Brotherhood leaders accuse the military of deliberately sabotaging their time in office and plotting their demise. After two pro-Morsi protest camps were crushed by police on Wednesday, the Brotherhood launched a "Day of Rage" on Friday, and clashes left at least 173 dead. They have urged their supporters to take to the streets daily in the week ahead.
There were no reports of major rallies on Saturday. The interior ministry said police had arrested more than 1,000 Muslim Brotherhood "elements" following Friday's riots.
The group said daughters and sons of the leadership had been targeted in an effort to gain leverage over the organisation. The state news agency said 250 Brotherhood followers faced possible charges of murder, attempted murder and terrorism.
The government has ordered a dawn-to-dusk curfew that looks set to last until the middle of September, leaving the normally crowded streets of major cities eerily deserted at sundown.
Looking to regain some semblance of normality, banks were due to re-open on Sunday for the first time since Wednesday's carnage, and the stock exchange will also resume business, with trading cut to three hours from four because of the instability.
Gun battle in Cairo mosque as Egypt mulls Brotherhood ban
Security forces cleared a Cairo mosque after a gun battle with followers of the Muslim Brotherhood on Saturday, while Egypt's army-backed government, facing deepening chaos, considered banning the Islamist group.
Reuters witnesses saw gunmen shoot from a window of the al-Fath mosque, where supporters of deposed president Morsi had taken shelter during ferocious confrontations in the heart of the Egyptian capital on Friday.
Another gunman was shown on television shooting from the mosque's minaret and soldiers outside returning fire. Hours later, police moved in and secured the building, making scores of arrests as crowds on the streets cheered them on.
It was not clear if anyone died in the clashes - the fourth day of violence which has killed more than 700 people.
Trouble was also reported in the second city Alexandria. An office run by the Muslim Brotherhood was set ablaze and a security source said a Morsi supporter was killed.
The health ministry said 173 people died in clashes across Egypt on Friday, including 95 in central Cairo, after the Brotherhood called a "Day of Rage" to denounce a crackdown on its followers on Wednesday that killed at least 578 people.
Among those killed was a son of Muslim Brotherhood leader Mohamed Badie, shot dead near the al-Fath mosque. Fifty-seven policemen have also died over the past three days, the interior ministry said.
The authorities said they arrested more than 1,000 people after Friday's protests, and one handcuffed man was shown on television with a gun on his lap. The state news agency said 250 Brotherhood followers faced possible charges of murder, attempted murder and terrorism.
Security sources said Mohamed Al-Zawahiri, the brother of al-Qaeda leader Ayman Al-Zawahiri, had also been detained.
Brotherhood spokesman Gehad El-Haddad said on Saturday the police had started to arrest the sons and daughters of the organisation's leadership.
Despite the bloodshed, the Islamist group has urged its supporters to take to the streets every day this next week, but there was no sign of large rallies by late Saturday.
"Our rejection of the coup regime has become an Islamic, national and ethical obligation that we can never abandon," said the Brotherhood, which has accused the military of plotting the downfall of Morsi to regain the levers of power.