Of the 48 suspects, 31 are in custody and 17 still at large, it said.
IS claimed responsibility for the three suicide attacks that targeted the churches in December and April.
A December 11 attack in the heart of Cairo on the Saint Peter and Saint Paul church, adjacent to the headquarters of Coptic Pope Tawadros II, killed 29 people.
On April 9, 45 people were killed in twin church bombings claimed by IS as Christians gathered to celebrate Palm Sunday in the cities of Tanta and Alexandria.
IS has threatened to carry out more attacks against Egypt's Christians, who make up around 10 percent of its population of about 90 million.
The suspects allegedly set up IS cells in Cairo and in the southern province of Qena, the statement said.
It added that they were also suspected of undergoing training at IS military camps in Libya and Syria.
The group is also accused of killing eight policemen and wounding three at a checkpoint in the southwest on January 16, the statement said.
Since last month's church attacks, the interior ministry has issued regular statements announcing the arrest of IS suspects in connection with the bombings.
