"I am appealing to all Muslim religious leaders and communities to understand the statement of Pope Benedict XVI," the mayor said.
Duterte, known to have a good rapport with the city's Muslim community, said the Pope did not intend to give an anti-Islam speech and was misquoted.
"I appeal for people to read first the whole speech of the Pope," he said, although admitted having not read the speech himself but noted that the speech has direct English translations.
Aleem Mahmod Adilao, the regional chair of the Ulama League of the Philippines, said he does not believe the Pope intended to have anti-Islam pronouncements.
"We know he stood for inter-religious dialogue. It's impossible he has a bad intention," the Muslim cleric said in Testigo, a GMA television news program here.
Adilao said reactions to the Pope's speech were fueled by bloated reports in the media.
The Iglesia Independiente Filipinas also said in Testigo that the Pope did not intend to give "anti-Islam" remarks. "Let us give him a chance for understanding so there will be unity," one of the church's bishops said.
Pope Benedict XVI said on Sept. 17 that he is "deeply sorry" about the reaction to his speech. He quoted a 14th-century Byzantine emperor as saying that the prophet Muhammad brought "only evil and inhuman" things to the world.
The pope said that the quotation does not show his personal stand and that the speech was intended to invite inter-religious dialogue "with great mutual respect."