Both as a curial official and since becoming a bishop, he has conducted investigations into sexual abuse by clergy on behalf of the Holy See and led a board that reviews such cases.

Since November 2018, Scicluna has been an Adjunct Secretary of the Dicastery for the Doctrine of the Faith, the curial body responsible for dealing with clerical sexual abuse cases on minors around the world.

[10] At a prayer service for priests in St Peter's Basilica in May 2010, Scicluna addressed the clerical vocation and said:[11] The child becomes the model for the disciple who wants to be "great" in the kingdom of heaven.... How many are the sins in the church for arrogance, for insatiable ambition, the tyranny and injustice of those who take advantage of ministry to advance their careers, to show off, for reasons of futile and miserable reasons of vanity!

All this makes the child precious in God's eyes, and in the eyes of a true disciple of Jesus.He went on to quote the gospels on the corruption of the young–"Whoever causes one of these little ones who believe in me to sin, it would be better for him if a great millstone were hung around his neck and he were thrown into the sea" (Mark 9:42)–and then quoted Gregory the Great's exegesis of that verse's meaning for priests:[11] Mystically expressed in the millstone is the hard and tedious rhythm of secular life, while the deep sea signifies the most terrible curse.

Without a doubt, if they had fallen all by themselves, their suffering in Hell would be easier to bear.Addressing a conference on sexual abuse held in February 2012 at the Pontifical Gregorian University, he explained that the CDF needed the support of the entire church hierarchy for its procedures to have their intended impact: "No strategy for the prevention of child abuse will ever work without commitment and accountability."

He said that "the deliberate denial of known facts, and the misplaced concern that the good name of the institution should somehow enjoy absolute priority" were "enemies of truth" and reflected "a deadly culture of silence" which he characterized as a form of omertà, the word used to describe the Mafia's code of silence to protect criminal conspiracies in the face of civil and criminal authority.

[15] The Holy See announcement described him as "highly respected among his peers around the world for his lecturing skills and his expertise in child protection issues".

[7] In an interview on the eve of his departure from Rome, Scicluna said the move was a promotion and not a manifestation of departmental rivalries within the Holy See.

[17] On 1 December 2012 Pope Benedict XVI appointed Scicluna to a renewable five-year term as a member of the Congregation for the Doctrine of the Faith.

[18][b] In April 2014 Scicluna was appointed by the Holy See to take the testimony of clergy alleging sexual misconduct in the Archdiocese of St Andrews and Edinburgh.

[27] On 30 January 2018, after Pope Francis was sharply criticized for controversial comments about the clergy sex abuse scandal in Chile, he sent Scicluna to conduct an investigation and take statements from victims who charged that Msg.

Juan Barros, whom Francis named Bishop of Osorno in 2015, had personal knowledge of their abuse years earlier.

[29] During the Meeting on the Protection of Minors in the Church, Italian journalist Sandro Magister asked Scicluna why the term “homosexuality” was absent from the opening day presentations of the summit.