Thirty-one of the suspects are in custody while the others are still at large.
More than 70 people died in suicide attacks against churches in Cairo in December and in the cities of Tanta and Alexandria in April.
IS said it carried out the bombings.
In a statement on Sunday, public prosecutor Nabil Sadek said some of the suspects were leaders within IS and had formed cells in Cairo and the southern province of Qena to carry out the church attacks.
The attack in December killed 29 people at Saint Peter and Saint Paul Church in central Cairo, close to the headquarters of Coptic Pope Tawadros II.
In April, 45 worshippers celebrating Palm Sunday died in attacks at St George’s Coptic church in Tanta and St Mark’s in Alexandria.
IS has threatened more attacks on Egypt’s Coptic Christians, who make up 10% of the population.
Egypt’s President Abdul Fattah al-Sisi announced a three-month state of emergency after the attacks in April.