Egypt's beleaguered Christian minority make up around 10% of the population.
The two attackers opened fire at the entrance to the church of Mar Mina in Helwan district, which was being guarded by police in the run-up to Orthodox Christmas celebrations next week, security sources said. Including the dead attacker, at least three people were involved in the terrorist squad.
The Islamic State asserted responsibility for Friday's assault.
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Five security guards were also wounded in the rampage outside the church south of the capital Cairo before a gunman was shot dead as he tried to storm the building.
Police have stepped up security measures around churches ahead of Coptic Christmas celebrations on January 7, deploying officers outside Christian places of worship and setting up metal detectors at some of the bigger churches. Police have been stationed outside churches and in nearby streets across Cairo.
A video circulating on social media after Friday's attack apparently showed the gunman lying on the ground with his face covered in blood.
Al-Sisi said that he "is following the consequences of the terror attack closely". "There was more than one attacker", Mohammed Hussein Abdelhadi, who lives close to the church, told Reuters. It is centered in the turbulent northern part of Sinai but has also carried out attacks in the mainland.
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