Archbishop Orlando Quevedo of the Archdiocese of Cotabato condemned the attack outside the Cathedral of the Immaculate Conception as people were leaving Mass, calling it a "sacrilege."
"The church they attacked is a place of refuge, even for criminals," he told the local Manila Bulletin. "People were worshiping when the bomb went off. This is not just a crime, this is a sacrilege."
The pope also condemned the violence while praying for the victims.
"While I pray to God for the victims of this ignoble gesture, I raise my voice to condemn yet again the recourse to violence, which is never a worthwhile way to solve existing problems," Pope Benedict XVI told pilgrims in St. Peter's Square.
According to Cotabato City Mayor Muslimin Sema, authorities arrested a male they suspected to be the bomber minutes after the blast.
While some have accused the 11,500-strong Moro Islamic Liberation Front for the attack, a spokesman for the group has denied involvement and also condemned the bombing.
He said the rebels would not do anything to foment a religious war though the militant group has been fighting to establish a separate Islamic state.