All 24 serving bishops in the Catholic Church in Ireland were summoned to the talks, held at the Apostolic Palace in the wake of last year's reports detailing decades of unreported child abuse and deliberate concealment on the part of the Church to protect its own reputation.
The Vatican said in a statement that the Pope had urged the bishops to take concrete steps to bring healing to victims of the abuse, encourage a renewal of faith in Christ, and restore the Church's spiritual and moral credibility.
The Pope said the crisis was linked to a lack of respect for the human person and a weakening of faith within the Church, as he denounced the sexual abuse of children as a "heinous crime" and "grave sin that offends God and wounds the dignity of humans who are made in his image".
The Pope said the bishops needed to engage in deeper theological reflection in the wake of the scandal and improve the spiritual, pastoral and academic preparation of candidates for the priesthood.
The bishops acknowledged that the crisis had led to a breakdown in trust in the Church and damaged its witness to the Gospel.
They told the Pope of the anger and sense of betrayal expressed to them by those who had been abused at the hands of parish priests and clergy in Church-run institutions.
Part of the meeting was given over to discussing the pastoral letter being prepared by the Pope for Catholics in Ireland. The Vatican said the letter would be published before Easter.
The delegation to the Vatican included Primate of All Ireland Archbishop Sean Brady and the Bishop of Galway Martin Drennan, the only one of five bishops named in the Murphy report not to have resigned. He has clung to his position in spite of repeated calls from victims for the resignation of all clergy who failed to act on the abuse.
The meeting concluded as the papal nuncio to Ireland, Cardinal Giuseppe Leanza, came under fire for telling a parliamentary panel that he would not answer questions on the abuse scandal.
In a letter sent to the lawmakers yesterday, Cardinal Leanza said: "I wish to inform that it is not the practice of the Holy See that apostolic nuncios appear before parliamentary commissions."