The al-Azraa church went up in flames during the clashes
Egypt's justice minister has warned that those who threaten the country's security will face "an iron fist".
Abdel Aziz al-Gindi was speaking after 12 people died and more than 180 were wounded during clashes between Muslims and Christians in Cairo.
More than 190 people detained after the fatal clashes will face military trials, Egypt's army says.
The ruling Supreme Council of the Armed Forces called the move a "deterrent" against further violence.
"The government's hand is not shaking. The government is not weak," Mr Gindi said, speaking after an emergency cabinet meeting convened by Prime Minister Essam Sharaf.
Mr Sharaf postponed a visit to the Gulf to hold the meeting.Continue reading the main story Analysis Jonathan HeadBBC News
For months conservative Muslim groups in Egypt have been protesting about the case of Camelia Shehata, the wife of the Coptic priest, who vanished last year. They say she converted to Islam and was being held against her will. But she has now appeared on a TV channel saying she is still a willing Christian.
Last night's attack by a Salafi crowd on the Saint Mena church in Imbaba was about a different woman, who they also allege is being forcibly prevented from converting to Islam.
Prime Minister Essam Shara is sufficiently alarmed by the scale of the violence to cancel his trip to the Gulf.
Some Egyptians believe the military deliberately allows the fighting to continue because it is unwilling to confront the Salafis, who have become more assertive since the fall of. Some believe it is elements of the old regime stirring up trouble. Certainly there are ambitious figures in both communities whose leadership aspirations might benefit from increased strife
Heightened political competition in the run-up to the first post-Mubarak election in September could well spark off more communal clashes. The interim military government's track record in dealing with them, is not encouraging.
Mr Gindi said the government would "immediately and firmly implement the laws that criminalise attacks against places of worship and freedom of belief", which would allow for the death penalty to be applied.
He said the Egyptian people, police and army were "standing together to foil the counter-revolution", following the popular protests that unseated the government in February.Fire bombs
Saturday's violence started after several hundred conservative Salafist Muslims gathered outside the Coptic Saint Mena Church in Cairo's Imbaba district.
They were reportedly protesting over a months-old allegation that a Christian woman was being held there against her will because she had married a Muslim man and wanted to convert to Islam.
However, the woman had dismissed the allegations in an interview on a Christian TV channel.
Witnesses said the confrontation began with shouting between protesters, church guards and people living near the church.
Rival groups threw fire bombs and stones, and gunfire was heard.
The church and one other, as well as some nearby homes, were set alight, and it took hours for the emergency services and the military to bring the situation under control.
On its Facebook page, the Egyptian army announced: "The Supreme Military Council decided to send all those who were arrested in yesterday's events, that is 190 people, to the Supreme Military Court."
It added that it should act as a "deterrent to all those who think of toying with the potential of this nation".At least one church was damaged by fire during the protests
The statement also said that a committee would be set up to assess the damage caused by the clashes and "restore all property and places of worship to how they were".
The army warned of "severe dangers facing Egypt during this phase".
Saturday's clashes were not the first outbreak of communal violence since President Hosni Mubarak left office in February following weeks of popular protests.
During the protests in Cairo, many Christians and Muslims had protested alongside each other and protected each other during prayer times.
But in March, 13 people died in sectarian clashes in another neighbourhood. Last month, demonstrators in the southern city of Qena cut all transport links with Cairo for a week in protest over the appointment of a Christian governor.
The clashes - coming as the military government leads a faltering transition to democracy - are a worrying development for Egypt, the BBC's Jonathan Head in Cairo says.
Salafist groups - who have made similar claims about women being held against their will before - have become more assertive in the post-Mubarak era, he adds.
Coptic Christians account for about 10% of Egypt's population, and have long complained of state discrimination against them.
Now they are expressing fears for their safety if hardline Muslims do well in the election scheduled for September, our correspondent reports.