His profane remarks have set the leader on a collision course with Asia's largest Catholic Church.
Archbishop Romulo Valles, who heads the country's association of bishops, called for a day of prayer on 16th July to invoke "God's mercy and justice on those who have blasphemed God's holy name, those who slander and bear false witness and those who commit murder or justify murder as a means for fighting criminality".
He asked Filipino Catholics to join bishops in three more days of fasting, prayer and almsgiving starting on 17th July.
His statement, which did not mention President Duterte's name, added: "The Church respects the political authority, especially of democratically-elected government officials, as long as they do not contradict the basic spiritual and moral principles we hold dear, such as respect for the sacredness of life, the integrity of creation, and the inherent dignity of the human person."
On Friday, Mr Duerte vowed to resign from his position if someone could prove God is real though a selfie.
"I just need one witness who will say, 'Those fools at the church ordered me to go to heaven and talk to God. God really exists. We have a picture together and I brought a selfie'," he said during the opening of a science and technology event.
A week prior he used an expletive to describe God and called him "stupid".
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.