Rodrigo Duterte drew criticism from political and religious leaders alike in the staunchly Catholic nation for the comment he made in a recent speech.
The 73-year-old was quoted by The Manila Times as saying "I will not do that, not in a million years," during a media interview in the central province of Bohol.
A letter sent to the leader on Monday by the Philippines for Jesus Movement - which claims to represent ten million people - urged him to say sorry.
Duterte questioned the biblical account of creation - specifically why God made Adam and Eve only to let them to succumb to sin.
Mr Duterte asked: "Who is this stupid God? This son of a ***** is then really stupid."
Opposition senator Antonio Trillanes IV branded Duterte - who has launched outspoken attacks on other public figures including the pope - an "evil man".
The politician said his comments were "very much consistent with the deceitfulness, heartlessness and ruthlessness of his policies".
Meanwhile, the Catholic Bishop Arturo Bastes called for prayer to put a stop to Duterte's "blasphemous utterances".
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