Saturday's clashes erupted after a group of Muslims attacked the Coptic Saint Mena church in the northwestern district of Imbaba to free a Christian woman they alleged was being held against her will because she wanted to convert to Islam.
The verbal clash soon developed into a full fledged confrontation where the two sides exchanged gunfire, firebombs and stones.
Hermina, a parish priest, told AFP news agency that the dead were Copts who died when "thugs
and Salafists fired at them" in the late afternoon attack.
The church floor was bloodstained as wounded Christians were brought in for treatment.
Authorities deployed large numbers of soldiers and police, backed by armoured vehicles, to the area. The army fired shots in the air and used tear gas to separate both sides, witnesses said.
Interfaith relationships often cause tension in Egypt, where Christians make up about 10 per cent of its 80 million people.
Call for calm
The strife represents another challenge to Egypt's military rulers who are trying to restore law and order after President Hosni Mubarak was forced to step down in a popular uprising in February.
The Grand Mufti of Egypt Ali Gomaa, a senior Islamic religious figure, called for calm.
"All Egyptians must stand shoulder to shoulder and prevent strife," he told the state MENA news agency.
He also urged the military council to stop anyone from meddling with the security of Egypt.
Christians complain about unfair treatment, including rules they say make it easier to build a mosque than a church.
Claims that Christian women who converted to Islam were kidnapped and held in churches or monasteries have soured relations between the two communities for months.
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