Archbishop Louis Urshalimi made the remark in a meeting with Iranian Ambassador to Lebanon Ghazanfar Roknabadi.
Urshalimi said despite Cairo's ties with Tel Aviv, Coptics in Egypt have so far refused to recognize the Israeli regime as a state.
Roknabadi, for his part, condemned the church attack and the perpetrators behind it. The Iranian envoy also expressed sympathy for the families of those killed in the terror attack.
At least 21 people lost their lives and more than 70 others were injured when an explosive-laden vehicle, targeting a New Year's Eve service at the al-Qiddissin Church, detonated.
No group has yet claimed responsibility for the deadly attack.
Egyptian investigators issued a report on Monday saying the bomber probably intended to detonate his bomb inside the building to kill as many people as possible, but police guards had prevented the attacker from gaining entry into the house of worship.
Earlier on Saturday, Iranian Foreign Ministry issued a statement condemning the attack.
Iranian Foreign Ministry Spokesman Ramin Mehmanparast denounced, in a statement, the death of innocent people during the blast and offered his condolences to the people and government of Egypt.
Palestinians have also strongly condemned the attack and blamed the deadly terrorist act on Israeli intelligence agencies.
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