However, he refused to engage in a word war with Duterte, opting to give a message of hope.
"Mine is the silence of Jesus before the arrogance of Pilate," Villegas said Sunday. "Mine is the language of peace that refuses the dark magic of revenge. Mine is the silence of respect for those who consider us their enemies but whose good we truly pray for and whose happiness we want to see unfold."
"There is virtue in silence. There is virtue in speech. Wisdom is knowing when it is time for silence and when is the timing for speech," he added.
Duterte has dubbed the Catholic Church the "most hypocritical institution" as he lambasted its bishops for supposedly attempting to erode public support for him before the May 9 elections.
He also cited the release of a pastoral letter a few days before the elections in a bid to dissuade the electorate from voting for him.
"They campaigned against me, everybody was saying 'Do not vote for Duterte.' Fine. I said, let this election be a referendum between me and the Catholic Church... Sabi ko, this will be a referendum kung sinong tama sa atin. Look, were you able to stop me? Iilan lang kayong mga obispo diyan," he said.
Duterte also singled out Oscar Cruz, the retired archbishop of the Archdiocese of Lingayen-Dagupan, for, according to him, making a fool out of the Filipino people.
Villegas believes Catholics will understand his decision to stay silent.
"You can understand my speech if you speak the language of silence. You can understand my silence if you know how to love like Him who was born one silent night," he said.