At least 25 people were killed in Cairo and 272 were reportedly injured, when troops broke up a protest, deepening public doubt about the military's ability to steer the country peacefully towards democracy, Reuters reported.
In the worst violence since Hosni Mubarak was ousted, armoured vehicles sped into a crowd late on Sunday (9 October) to crack down on a protest by Coptic Christians near Cairo's state television. They took to the streets after accusing Muslim radicals of partially demolishing a church in Aswan province last week.
Online videos showed mangled bodies and activists said some people were crushed by wheels.
Tension between Muslims and minority Coptic Christians have simmered for years. Relations have worsened since the anti-Mubarak revolt, which gave a freer rein to Salafist and other radical Islamist groups that the former president had repressed.
Christians make up 10 percent of Egypt's roughly 80 million people.
According to Stratfor, the global intelligence website, the state media exacerbated the tensions by blaming the Copts for the violence. The media exhorted people to go on the streets and defend the army from the Copts.
According to the website, the violence on Sunday has been a turning point: until now, violence against the military had been unthinkable, and the military had avoided using this much force against the demonstrators.
Prime Minister Essam Sharaf, appearing on state TV in the early hours on Monday, said the government's attempts to build a modern, democratic state were being disrupted by security concerns and talk of plots against democracy.
"We will not surrender to these malicious conspiracies and we will not accept reverting back," he said before the interim cabinet met and launched an investigation into the violence.
Catherine Ashton, the EU High Representative for Foreign Affairs, expressed her "extreme concern" by the large number of deaths and injuries among the Coptic Christian community, resulting from the violent clashes in Egypt.
"Freedom of religion or belief is a universal human right, which needs to be protected everywhere and for everybody. It must be an essential part of the transition to democracy as Egypt builds a free and democratic society," Ashton stated.
Many liberal politicians and Egyptians have been worried by the rising influence of the Muslim Brotherhood since the February uprising. Voting in a parliamentary election in Egypt starts on 28 November.
Cartoon sparks fire in Tunisia
In Tunisia, the first Arab country to oust its authoritarian ruler last January, and where the first democratic elections are due on 23 October, Islamists attacked a TV station which had shown the award-winning cartoon film Persepolis.
Persepolis, which was broadcast on Friday by the channel, is a French-Iranian animation feature based on an autobiographical graphic novel by Marjane Satrapi. It depicts the last days of the Shah and Iran's 1979 Islamic Revolution.
The protesters are angered by fantasy scenes in which God is shown talking to a young girl.
Officials quoted by the BBC said the activists had tried to set Nessma TV station on fire after it broadcast the animation, which they deem to be blasphemous.
Police clashed with other Islamists who want a ban on women wearing the niqab at university lifted, reports say.
The protests come ahead of elections for a constitutional assembly. The poll, in two weeks' time, will be the first vote in Tunisia since long-time President Zine al-Abidine Ben Ali was toppled in January.
Correspondents say that since Ben Ali's autocratic government has been toppled, more conservative Muslims are making themselves heard.