Gunshots rang out at the scene outside the state television building, where lines of riot police with shields tried to hold back hundreds of Christian protesters chanting "This is our country." Thick black smoke filled the air from the burning vehicles. Security forces eventually fired tear gas to disperse the protesters.
An Interior Ministry official at the scene told The Associated Press that two people had been killed, but he did not say who they were or how they died. State television said 30 soldiers were injured.
Thugs with sticks chased the Christian protesters from the site, banging metal street signs to scare them off. One soldier collapsed in tears as ambulances rushed to the scene to take away the injured. Television footage of the riots showed some of the Coptic protesters attacking a soldier, while a priest tried to protect him.
The trouble began when thousands of Coptic Christians protesting the latest attack on a church in southern Egypt came under attack as they chanted denunciations of Egypt's military rulers, whom they accuse of leniency in dealing with a series of anti-Christian attacks.
"The people want to topple the field marshall," the protesters yelled, referring to the head of the ruling military council, Field Marshall Hussein Tantawi.
The rally began in the Shubra district of northern Cairo, then headed to the state television building overlooking the Nile where men in plainclothes attacked the Christian protesters. It was not immediately clear who the attackers were.
Egypt's Coptic Christian minority makes up about 10 percent of the country's population of more than 80 million people. As Egypt undergoes a chaotic power transition and security vacuum in the wake of this year's uprising, Christians are particularly worried about the increasing show of power by the ultraconservative Islamists.
"Our protest is peaceful and I don't know why they attack us," said Rami Kamel, a Coptic protest leader.
In the past 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 local ultraconservative Muslims, called Salafis, that a cross and bells be removed from the building.
Aswan's governor, Gen. Mustafa Kamel al-Sayyed, further raised tensions by telling the media that the church was being built on the site of a guesthouse, suggesting it was illegal.
Kamal, the protester, said the Copts demand 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.
Last week, security forces used force to disperse a similar protest in front of the state television building. Christians were angered by the treatment of the protesters and vowed to renew their demonstrations until their demands are met.
In other developments, the ruling military council ordered a halt to trials of civilians before military courts known for swift and harsh verdicts. The military trials have drawn harsh condemnation from protesters and youthful activists behind the uprising, who claim that reform is not coming fast enough or extensively enough.
However, those who violate military laws, such as assaulting servicemen or damaging military installations, would still be referred to military tribunals.
Rights groups say at least 11,000 civilians have been tried before military tribunals since the February ouster of Hosni Mubarak. Tantawi chairs a military council that took control of the country from Mubarak with pledges to return Egypt to civilian rule after a transition period.
The rights groups also claim the military tortures detainees.