Mr. Duterte has repeatedly accused the church of hypocrisy, suggesting that many of its priests had affairs with women. After a Philippine priest was gunned down this month — the third killing of a priest since December — Archbishop Villegas urged Mr. Duterte to tone down his criticism of the church, saying it could encourage such attacks, but he refused.
In April, the president said he had ordered the arrest and deportation of an Australian nun, Sister Patricia Fox, who had joined street protests condemning the antidrug killings. The Justice Department nullified the order this month, telling the country’s immigration bureau to review the case.
Mr. Duterte has joked more than once that he intended to start a new religion with himself as the leader, the sole purpose of which would be to create happiness.
Many of Mr. Duterte’s political allies are Protestants, including Senator Manny Pacquiao, the former boxing champion, who is an evangelical Christian. Mr. Duterte also enjoys the backing of the Iglesia Ni Cristo, a Christian sect that is a political force in the country.
On Tuesday, the Philippine Council for Evangelical Churches joined the criticism of Mr. Duterte’s remarks, calling on the president to “refrain from issuing insulting statements against the Christian faith.”
“History teaches us that religious intolerance can lead to animosity and violent conflict,” said the group, which says it represents about 30,000 evangelical churches in the country.
In a sign that Mr. Duterte hoped to defuse the controversy, his spokesman, Harry Roque, said the government had created a panel to reach out to the Catholic Church in hopes of sorting out their differences.
“We know that there is a separation of the powers of state and church and that there is no need for a dialogue, but the president thought it wise to open our doors to dialogue,” Mr. Roque said Tuesday.