The the government views as "interference" in its affairs remarks made by Pope Benedict XVI voicing support for the Copts since the deadly New Year's Eve attack on a Coptic Christian church in northern Egypt.
"Egypt asked its ambassador in the Vatican to come to Cairo for consultations after the Vatican's new statements that touch on Egyptian affairs and which Egypt considers an unacceptable interference in its internal affairs," foreign ministry spokesman Hossam Zaki was quoted as saying in a statement.
"Cairo is keen to communicate with the Vatican after its statements following the terrorist incident in Alexandria that took place earlier this month," the statement added.
Pope Benedict XVI has repeatedly expressed solidarity with the Copts and called on world leaders to protect them in the aftermath of the church bombing that killed 23 people and injured nearly 80 others as worshippers emerged from midnight mass in Alexandria.
The pontiff in an address in Rome on 2 January deplored the Alexandria attack as a "vile gesture". He issued fresh condemnation of the attack and the insecurity faced by minorities in Egypt and elsewhere in a speech on religious freedom which he gave Monday to diplomats in Rome.
"In Alexandria, terrorism brutally struck Christians as they prayed in church. This succession of attacks is yet another sign of the urgent need for the governments of the region to adopt, in spite of difficulties and dangers, effective measures for the protection of religious minorities," Benedict said in the speech.
Copts have been previously been targeted in Egypt and the Alexandria attack followed an October bombing of a cathedral in the Iraqi capital Baghdad that killed 58 people including two priests and injured scores.
The Baghdad blast was claimed by an Al-Qaeda linked group and the Egyptian government has said it suspects the Alexandria blast was the work of an foreign extremist plot.