Rodrigo Duterte, who has in the past insulted the pope and former US president Barack Obama, was called an "evil man" by opposition senator Antonio Trillanes IV.
The senator said the president's remarks are "very much consistent with the deceitfulness, heartlessness and ruthlessness of his policies".
Even some of Mr Duterte's allies voiced criticism.
Catholic Bishop Arturo Bastes sought prayers to end Mr Duterte's "blasphemous utterances".
In a speech, Mr Duterte questioned the biblical story of man's creation and asked why God created Adam and Eve only to allow them to succumb to temptation that destroyed their purity.
Mr Duterte asked: "Who is this stupid God? This son of a ***** is then really stupid."
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