Security forces reportedly shot and killed one of the attackers who was carrying an undetonated explosive belt after an exchange of fire and another was arrested.
According to the Youm7 newspaper, the security forces are now trying to detain the second attacker, who left the scene riding a motorcycle.
Egypt's state-run MENA news agency, citing an unnamed official at the Interior Ministry, said Friday's attack in the Helwan neighborhood was carried out by two assailants; one of them fled the scene and was being chased down.
Authorities reported at least nine people dead, among them three police officers.
Two men on a motorcycle opened fire and tried to storm the Mar Mina church in Helwan City on Friday, which led to a shootout between the attackers and security officers, according to Egypt's Health Ministry spokesman.
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Among those killed were eight Christians and a Muslim, officials said.
Cellphone footage posted on social media appeared to show the bearded gunman wearing a bulky ammunition vest sprawled on a street, barely conscious, as people restrained his arms and then handcuffed him.
The church was being guarded by police in the run-up to Orthodox Christmas celebrations next week.
Coptic Christians in Egypt have been faced several attacks by extremist organisations.
A witness who did not want to give his name said a policeman was killed while he was closing the church gate to stop the gunman getting in.
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Egypt's Coptic Christians make up about 10 percent of the country's 93 million people, and are the largest religious minority in the region.
President Abdel Fattah al-Sisi offered his condolences to the families and ordered security forces to increase safety measures at sensitive sites, his office said in a statement.
Security forces have put checkpoints in place around the capital in response to the attacks.
The attack killed an aide to the defense minister and a helicopter pilot, but both ministers returned to Cairo unscathed.
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