The statement followed Wednesday's clashes with security over a decision to stop construction on a Giza church. Authorities claim the church lacked the required permits.
The violence left one Copt dead and scores injured.
"God gives authority to some people so they can give comfort to those under their rule, but authority should not be violently exercised," Shenouda said in his weekly address.
Egypt's general prosecutor vowed to punish those involved in the unrest.