Duterte draws the ire of the public often for his remarks mocking and questioning the beliefs of the Catholic Church, the dominant religion in the Philippines.
The people of God "should come to know us as friends of their safety and that of their children and youth", he said.
He called for specific protocols to handle accusations against bishops, in yet another reference to the McCarrick scandal. "That can no longer go on. this is a make or break time for the Church". "The question of pedophilia is not a question of religion, it is (a question of) crime", Francesco Zanardi, head of the main victims advocacy group in Italy Rete L'Abuso, or Abuse Network, told a news conference in the Italian parliament.
Juan Carlos Cruz, a Chilean, said on the video that when he reported abuse to religious authorities he was treated as a liar and an enemy of the Church.
The almost 200 bishops, cardinals and heads of religious orders attending the conference were addressed by victims of predatory priests, with one telling them bluntly: "You are the physicians of the soul and yet, with rare exceptions, you have been transformed into murderers of the soul".
Speaking to the BBC, Brigitte, who had been abused by a chaplain, said she was initially afraid to tell people about her story because she was told she would "never become an angel in heaven".More news: Karl Lagerfeld may have willed $3.4 million to his cat
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"Our lack of response to the suffering of victims, even to the point of rejecting them, and covering up the scandal to protect the perpetrators and the institution, has injured our people", he said.
"We turn to you with deep distress!"
But critics say it may be too little, too late, both for the credibility of the church and Francis' pontificate.
The bishops from across the world heard harrowing video testimony from unnamed abuse survivors including from one woman who talked about how from the age of 15 she had sexual relations with a priest over the course of 13 years.
Leading prayers before the afternoon session of discussions, the Archbishop of Chicago, Cardinal Blase Cupich, recognised there are those who are still in denial about the abuse crisis in the Church.
The pontiff's brief address kicked off one of the most critical points of his papacy, a gathering of the world's leading bishops to discuss a problem that the Catholic Church for decades has struggled to curb - and that has now damaged the pope's own reputation. Jankowski is accused of molesting boys. World leaders including President George H.W. Bush and British Prime Minister Margaret Thatcher visited his church to recognize his anti-communist activity.