Egypt was on edge Monday after a night of sporadic violence outside Cairo's main cathedral following the death of seven people in clashes between Christians and Muslims.
Islamist President Mohamed Morsi has promised to launch an immediate investigation into the bloodshed.
Calm was restored outside St Mark's as police deployed in force at the cathedral in the central neighbourhood of Abbassiya, where several Coptic Christians were still gathered in the morning.
The death toll from the clashes outside the cathedral rose to two, according to an updated health ministry toll issued on Monday.
A day earlier, mourners had packed the cathedral for prayers to honour four Copts who had been killed in sectarian clashes in a town north of the Egyptian capital that also left one Muslim dead.
As the mourners left the cathedral, they came under attack from a crowd who pelted them with stones, sparking violence that killed another Christian, 30-year-old Mahrus Hanna Ibrahim Tadros.
The second person who died has not yet been identified.
Amid scenes of chaos, mourners rushed back into St Mark's to seek refuge as black-clad riot police began firing tear gas at the cathedral.
At least 89 people were wounded in the violence, the health ministry said.
Fresh fighting also erupted on Sunday between Christians and Muslims in Al-Khusus, the town north of Cairo where the trouble had started on Friday.
The bloodshed underscores simmering hostility that has often seen violence between Morsi's main Islamist allies and a broad opposition. It also highlights sectarian tensions that have been brewing for years.
During the funeral prayers, mourners holding up wooden crosses chanted against the powerful Muslim Brotherhood, from which President Morsi emerged, even as the bishops conducting the service called for peace and calm.
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Morsi, in a call to Coptic Pope Tawadros II, condemned the violence.
He ordered "an immediate investigation" into the clashes and condemned the violence as "an attack on myself", the official MENA news agency reported.
He also affirmed "the protection of all citizens, Muslims and Christians, is the responsibility of the state".
Catherine Ashton, the European Union's foreign policy chief who met with Morsi in Cairo on Sunday, said she contacted the presidency and called for restraint.
Hani Sobhi, a young Copt, explained live television coverage of the funeral had sparked the violence.
"Inside the cathedral we chanted 'Down with the Brotherhood rule' and that was aired live on television. At the exit (of the cathedral), the people were ready and waiting for us," he said.
The interior ministry said "a number of mourners began to damage cars in the area which led to confrontations with residents of the area".
Loud blasts were heard as rows of Abbassiya residents hurled rocks and bottles at the cathedral and were met in kind from Copts inside the complex.
Sunday's service was being held for the four Christians killed in the sectarian clashes two days earlier.
The violence in Al-Khusus, a poor area in Qalyubia province, flared on Friday after a Muslim in his 50s objected to children drawing a swastika on a religious institute.
The incident sparked rioting during which a church was partially burnt and a Christian's home torched.
Clashes in the town erupted again on Sunday evening, police said.
Christians form between six and 10 percent of Egypt's population of nearly 83 million people.