Thousands of people packed into Cairo's main Coptic cathedral Monday to mourn those killed in overnight clashes between Christian protesters and military police.

They gathered at St. Mark's in the Egyptian capital, a day after at least 25 people were killed and more than 200 injured in the worst street violence since the uprising that ousted Hosni Mubarak in February.

Egypt's Coptic church blasted authorities Monday for allowing repeated attacks on Christians with impunity.

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A woman grieves at a hospital morgue for protesters killed during clashes with Egyptian security forces in Cairo. (Associated Press)

Most of those hurt and killed were Christians who were trying to stage a peaceful protest in Cairo over a recent attack by Muslims on St. George Coptic Orthodox church, which is under construction, 1,000 kilometres south of Cairo.

"Strangers got in the middle of our sons and committed mistakes to be blamed on our sons," the Coptic church said in a statement. It lamented "problems that occur repeatedly and go unpunished."

The spiritual leader of the Coptic Christian minority, Pope Shenouda III, declared three days of mourning, praying and fasting for the victims starting on Tuesday and also presided over funerals for some of the Christians killed.

The clashes Sunday night raged over a large section of downtown Cairo and drew in Christians, Muslims and security forces. The violence began when about 1,000 Christian protesters were staging a sit-in outside the state television building.

Witnesses said two armoured vehicles ploughed through the crowd, crushing some of the demonstrators. The protesters said they were also attacked by "thugs" with sticks.

The violence spiralled out of control after a speeding military vehicle jumped onto a sidewalk. Video showed protesters chasing and then beating a man who had fled one of the vehicles.

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A Christian activist holds up a bullet belt, which he said was used by army forces during Sunday's clashes. (Associated Press)

Most of the people killed were Coptic Christians, though officials said at least three soldiers were among the dead. Egypt's official news agency said dozens have been arrested.

The European Union strongly condemned the violence.

Foreign call for religious tolerance

"It is about time that the Egyptian leadership understands the importance of religious plurality and tolerance," German Foreign Minister Guido Westerwelle said. "It's very important that the Egyptian authorities reaffirm freedom of worship in Egypt," added British Foreign Secretary William Hague.

Canadian Foreign Affairs Minister John Baird said in a statement released Monday that he was "very concerned" about the violence in Egypt and sent his condolences to the families of those killed "on behalf of all Canadians." 

"Religious extremism has no place in modern society and the new Egypt. Canada urges all involved to work together to build a society where religious communities can live and prosper together and build a new Egypt," he said.

"Freedom of religion is a fundamental human right and a vital building block for healthy democracies," Baird said. "People of faith must be able to practise and worship in peace and security."

Egyptian Prime Minister Essam Sharaf warned in a televised address that the violence was another setback on the country's already fraught transition to civilian rule after three decades of Mubarak's authoritarian government.

"These events have taken us back several steps," Sharaf said. He blamed foreign meddling for the troubles, claiming it was part of a "dirty conspiracy." Similar explanations for the troubles in Egypt are often heard from the military rulers who took power from Mubarak, perhaps at attempt to deflect accusations that they are bungling the management of the country.

"Instead of moving forward to build a modern state on democratic principles, we are back to seeking stability and searching for hidden hands — domestic and foreign  — that meddle with the country's security and safety," Sharaf said.

Riot police sent to hospital where bodies are kept

Violence resumed on Monday when several hundred Christians pelted police with rocks outside a Cairo hospital, where many of the Christian victims were taken the night before. Riot police were stationed outside the hospital.

The screams of grieving women rang out from inside the hospital and some of the hundreds of men gathered outside held wooden crosses. Empty coffins were lined up outside the hospital.

There were no word on casualties from Monday's clashes.

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Two armoured vehicles approach the crowd. (Reuters)

Eyewitness report

Sunday's violence began after Coptic Christians organized a protest march following an attack on one of their churches. ABC News reports they were joined by Muslim protesters, among them Tamir al Mihi of the Egyptian Social Democratic party, who had this to say about how it started:

"It was a very peaceful demonstration, no provocation on the part of the demonstrators, and all of a sudden we started hearing gunshots and the military police started  attacking the demonstrations with sticks and belts and firing at them. And then we saw two armoured vehicles chasing down the (inaudible), in front of the TV building at an unbelievable speed in the middle of the demonstrators and running them over, literally running them over."

Christians, who make up about 10 per cent of Egypt's 85 million people, blame the ruling military council for being too lenient on those behind a spate of anti-Christian attacks since Mubarak's ouster. The chaotic power transition has left a security vacuum, and the Coptic Christian minority is particularly worried about a show of force by ultraconservative Islamists, known as Salafis.

In recent weeks, riots have broken out at two churches in southern Egypt, prompted by Muslim crowds angry over church construction. One riot broke out near the city of Aswan, even after church officials agreed to a demand by ultraconservative Muslims known as Salafis that a cross and bells be removed from the building.

Aswan's governor, Gen. Mustafa Kamel al-Sayyed, further raised tensions by suggesting to the media that the church construction was illegal.

Christian protesters are demanding the ouster of the governor, reconstruction of the church, compensation for people whose houses were set on fire and prosecution of those behind the riots and attacks on the church.

Sunday's violence will likely prompt the military to further tighten its grip on power.

The ruling military council led by Field Marshal Hussein Tantawi, defence minister of 20 years under Mubarak's former regime, took over after the 18-day popular uprising forced Mubarak to step down. The military initially pledged to hand back power to a civilian administration in six months, but that deadline has passed, with parliamentary elections now scheduled to start in late November.

Conflicting reports

"The government first said this was a foreign conspiracy and there are spies. Then there was another report from the government saying the Coptic Christians attacked the military officers and took their guns and started using them against the other officers, and that's how three officers ended up dead. The Coptic Christians said this didn't happen, that this was a peaceful march until the military started running them over with their vehicles."

freelance reporter Marwa Rakha, reporting Monday from Cairo

According to a timetable floated by the generals, presidential elections could be held late next year.

Already, the military council said it had no intention to lift the widely hated emergency laws in place since Mubarak first took office in 1981.

Tension has been growing between the military and the youth groups that engineered the uprising, with activists blaming the generals for mishandling the transition period, human rights violations and driving a wedge between them and ordinary Egyptians.

"The army incites sedition to remain in power," said Mariam Ayoub, a relative of a slain Christian protester, Michael Mosaad, as she stood outside the Coptic hospital. "They tell all of us that this is what happens without emergency laws."

State television said authorities stepped up security at vital installations in anticipation of renewed unrest, deploying additional troops outside parliament and the Cabinet. Riot police were also stationed outside the Coptic hospital. Funeral services were planned in the afternoon at the main Coptic Cathedral in Cairo.

State television openly sides with army

The clashes on Sunday night did not appear to be exclusively sectarian.

State TV, which has been growing increasingly loyal to the military, appealed on "honourable" Egyptians to protect the army against attacks as news spread of clashes between the Christian protesters and the troops outside the TV building.

Soon afterward, bands of young men armed with sticks, rocks, swords and firebombs began to roam central Cairo, attacking Christians. Troops and riot police did not intervene to stop the attacks on Christians.

Throughout the night, the station cast the Christian protesters as a violent mob attacking the army and public property. At one point, Information Minister Osama Heikal went on the air to deny that the station's coverage had a sectarian slant, but acknowledged that its presenters acted "emotionally."

The military council ordered the Cabinet to investigate the violence and pledged measures to safeguard Egypt's security.