The clashes - in the suburb of Imbaba - came after Muslims attacked a church to free a Christian woman, witnesses said.
They alleged she was being held against her will because she wanted to convert to Islam.
Soldiers and police, backed by tanks, fired guns and tear gas to separate the groups, according to reports.
Eyewitnesses said some 500 conservative Muslims - known as Salafists - gathered at the Coptic Saint Mena Church in the northwestern Cairo suburb demanding to take custody of the woman.
Shouts were exchanged between church guards, people living near the church and the protesters, which developed into a fully-fledged confrontation during which the two sides exchanged gunfire, firebombs and stones.
"I just left one young man dead inside the church," one man, a Christian, was quoted as telling Reuters journalists.
A parish priest, Father Hermina, told the AFP news agency that the group had attempted to storm the church earlier in the day.
But one Muslim protester told the news agency that they had first been fired upon by the Copts.
"They started firing on us. We were peaceful," said the man, who gave his name as Mamduh. "We won't leave until they give up their weapons and the people who killed us are tried."
Relations between Egypt's Sunni Muslim majority and Coptic Christians - who account for about 10% of the population - have deteriorated in recent years.
I THINK WHAT GOING TO GO DOWN IN EGYPT MAY VERY WELL BE ON PAR WITH THE WORST PURGES IN HISTORY, IF NOT... A HOLOCAUST.
Clashes between Muslims and Christians in the Egyptian capital Cairo left six people dead and about 50 others injured, the health ministry said.
The two groups clashed in the northwestern district of Imbaba on Saturday after Muslims attacked the Coptic Saint Mena church to free a Christian woman they alleged was being held against her will because she wanted to convert to Islam.
A parish priest, Father Hermina, told AFP the dead were Copts who died when "thugs and (Muslim fundamentalist) Salafis fired at them" in the late afternoon attack.
The Gospel had been laid on a body wrapped in a sheet that was lying inside the church. The church floor was bloodstained as wounded Christians were brought into the church for treatment.
Outside the church, located in the poor working-class neighbourhood of Imbaba, military police parked several armoured cars to block off Muslim protesters from the church.
GEE... I WONDER IF THE ARAB LEAGUE WILL GO TO THE UNSCR TO ASK FOR AN INTERVENTION TO PREVENT VIOLENCE TO EGYPT'S CHRISTIANS!?
More than 190 people detained after fatal clashes between Muslims and Christians in Cairo are to face military trials, Egypt's army says.
The ruling Supreme Council of the Armed Forces called the move a "deterrent" against further violence.
Earlier the prime minister postponed a visit to the Gulf in order to hold an emergency cabinet meeting.
At least 10 people have died and 186 wounded during the overnight clashes in Cairo's Imbaba district.
... This is not the first outbreak of communal violence since the fall of President Hosni Mubarak in February following weeks of popular protests.
In March, 13 people died in similar 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.
ANY NEW REGIME IN EGYPT IS LIKELY TO BE MORE TOLERANT OF "SALAFISM" AND THIS WILL MAKE EGYPT LESS TOLERANT.
(YES: IMHO, MUBARAK WASN'T TOO HARSH ON THE SALAFISTS AND MUSLIM BROTHERHOOD; HE WAS TOO WEAK.
IF WE TRULY WANT GLOBAL PEACE AND UNIVERSAL BROTHERHOOD, THEN AS GERMANY ERASED NAZISM AFTER WW2, SO MUST ISLAMISM BE ERASED FROM THE ENTIRE GLOBE.)
The death toll from a sectarian clash over the alleged conversion of an Egyptian Christian woman to Islam rose to 12 on Sunday as the country's prime minister called an emergency cabinet meeting to discuss the violence.UPDATE #4 : TWO CHURCHES BURNED!
Witnesses said around 500 conservative Islamists known as Salafists massed outside the Saint Mina Church in the Cairo suburb of Imbaba on Saturday demanding that Christians hand over a woman they said had converted to Islam.
Following the emergency meeting, Egypt's government announced that it will step up security at religious sites and toughen laws that criminalize attacks on houses of worship.
Justice Minister Mohamed el-Guindy said the cabinet decided to activate laws dealing with terrorism, give police the resources they need to prevent inter-faith clashes and ensure those who vandalize houses of worship are severely punished.