Of the 48 suspects, 31 are in custody and the rest still at large, the general prosecutor's office said in a statement.
The attacks on a church in Cairo and two north of the Egyptian capital between December and April killed at least 75 people. A large number of people were wounded in the bombings.
IS claimed responsibility for the three attacks.
The first attack on December 11 on Saint Peter and Saint Paul church in Cairo killed 29 people.
The suspects have been accused of being leaders of the Islamic State terrorist group. They had also formed two terrorist cells in Cairo and the Upper Egyptian governorate Qena, public prosecutor Nabil Sadek said in the statement.
Christians, who have often been targeted by Islamist militants in Egypt, constitute around 10 per cent of its population of 900 million.
Egypt has seen a wave of deadly attacks by militants since 2013 when the military overthrew president Mohammed Morsi, an elected leader who hailed from the Muslim Brotherhood movement.
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