Vatican television showed each bishop thanking Francis at the end of their final meeting.
In a letter to the Chilean monsignors, Pope Francis said he had some "changes and resolutions" planned for the Catholic church as a result of the emergency sessions, which began May 15.
Francis summoned the entire Chilean bishops' conference to Rome for four days of meetings and prayer after admitting that he had made "grave errors in judgment" in the case of a Chilean bishop accused of witnessing and ignoring abuse.
"In the light of these painful events regarding abuses - of minors, of power and of conscience - we have realized the gravity of situation, as well as the tragic consequences that particularly victims have suffered", Pope Francis wrote, noting that seven additional bishops are likely to be removed as a means to re-establish confidence in the church.
Francis reiterated his heartfelt apology to the bishops and the victims, saying he is close to them and is united with them in "one single will and with the firm intention to fix the damages done".
After returning home, Francis sent two Vatican investigators to get to the bottom of the scandal, and they came back with a much broader view of the scale of abuse and cover-up in the Chilean church, presenting Francis with a 2,300-page dossier. The only one Francis is shown kissing on each cheek and patting on the arm was Bishop Juan Barros, who is at the center of the scandal.
In 2011, Karadima was convicted by the Congregation for the Doctrine of Faith of abusing minors and sentenced to a life of prayer and solitude.More news: In DR Congo identified 11 new cases of infection with Ebola
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In other cases, there was "grave negligence" in protecting children from paedophiles by bishops and religious superiors - a reference to the many cases of sexual abuse that have arisen in recent years within Chilean religious orders, including the Salesians, Franciscans and the Marist Brothers community.
The pontiff had strongly defended Barros who has been accused of covering up abuses by Fernando Karadima, another priest, in the 1980s and '90s.
Vira led a group of monks from Wat Phra Chetuphon Vimolmangklararm or Wat Pho, the Catholic Bishops' Conference of Thailand and Wat Pho's lay minister Thapana Sirivadhanabhakdi, Thai Beverage Ltd Co's CEO to the Vatican to strengthen the relationship between Buddhists and Catholic Christians.
After receiving the Scicluna-Bertomeu report, though, Francis did an about-face.
Greeting new ambassadors of Tanzania, Lesotho, Pakistan, Mongolia, Denmark, Ethiopia and Finland to the Holy See, Pope Francis said: "Among the most pressing of the humanitarian issues facing the worldwide community at present is the need to welcome, protect, promote and integrate all those fleeing from war and hunger, or forced by discrimination, persecution, poverty and environmental degradation to leave their homelands", said the Pope.
"The theme of the retreat is more of an ecclesial, theological theme which puts Christ in the center again, those things that we may have forgotten, the other things we have to continue doing", he said, explaining that all of the bishops, including Barros, were able to speak.