The protest came to an end on Monday after Egyptian security authorities agreed to hold a discussion on issues regarding the choice of faith of the two medical students who embraced Islam.
Coptic Christians and other minorities constitute about 6% of the population of predominantly Islamic Egypt.
Egyptian security authorities had initially refused to hand over the two Coptic Christian girls, who had announced their conversion to Islam to their families in al-Fayyum, Aljazeera said.
The girls may be transferred to a safe place in Cairo, sources told Aljazeera earlier on Monday.
A number of top Egyptian security officials had travelled to al-Fayyum in an attempt to investigate and resolve the dispute.
Sit-in at church
After learning that the girls had embraced Islam, several hundred agitated young Coptic Christians held a protest inside Mar Girgis church on Monday, chanting slogans against the conversion, according to Lina Ghadban, Aljazeera's correspondent in Egypt.
Some protesters speculated that the two girls, Marian Ayyad and Teresa Gorgy - both medical students at al-Fayyum general hospital - were pressured into changing their faith and were prevented from returning to Christianity.
The protesters say the girls were
pressured to embrace Islam
Egyptian security officials have, however, vehemently denied the accusation, saying that the girls had in fact notified the authorities concerned to officially announce and document their change of faith.
Not the first
The al-Fayyum incident comes only two months after a similar furore over a conversion incident.
In the previous case, a Coptic Christian woman's decision to embrace Islam triggered angry reactions from the community in Egypt. After discussions with the authorities, she renounced her decision.
During that incident, the Egyptian Coptic Christians' spiritual head, Pope Shenouda III, had secluded himself inside Wadi al-Natrun church after the arrest of some youths who were agitating inside the cathedral against the conversion.
The controversy persisted until the woman was returned to the Church and the detained youths released.