MANILA — Disparaging remarks about God by President Rodrigo Duterte have led to his sharpest clash yet with leaders of the Philippines’ politically powerful Roman Catholic Church, who on Tuesday accused him of attacking the beliefs held by the vast majority of the country.

“God has been called insulting names — words we always told you not to say or even write,” Archbishop Socrates Villegas said in a statement released Tuesday that was addressed to members of his archdiocese. “You are even being challenged to leave this church of your birth, the church of your grandparents.”

The archbishop was responding to a speech Friday in which Mr. Duterte cast doubt on the biblical story of creation, asking why God had created Adam and Eve only to let them be tempted and fall from grace.

“Who is this stupid God? This son of a bitch is then really stupid,” Mr. Duterte said. “How can you rationalize a God? Do you believe?”