Egypt has referred 48 people to the country's military judiciary for suspected involvement in three deadly church bombings and accused them of joining the Islamic State of Iraq and the Levant (ISIL, also known as ISIS) group.

Of the 48 suspects, 31 are in custody and 17 still at large, the public prosecutor's office said in a statement on Sunday.

ISIL claimed responsibility for the three suicide attacks that targeted the churches in December and April.

Two deadly church bombings in Alexandria and Tanta killed more than 45 people in April, months after a bombing near Cairo's Coptic Cathedral killed at least 25.

Public prosecutor Nabil Sadek said that some of the suspects held leadership positions in ISIL and formed cells in Cairo and the southern province of Qena to carry out the church attacks.

He added that they were also suspected of undergoing training at ISIL military camps in Libya and Syria.

The suspects are also accused of killing eight policemen and wounding three at a checkpoint in the southwest on January 16.

Egypt is fighting ISIL-linked fighters waging an insurgency focused in northern Sinai.

Attacks were largely against security forces in the sparsely populated Sinai Peninsula in the past, but the armed group has spread its violence to the mainland and increasingly targeted Christian civilians in recent months.