One case has come back to haunt him: An Italian priest who received the pope's clemency was later convicted by an Italian criminal court for his sex crimes against children as young as 12.
The Rev Mauro Inzoli is now facing a second church trial after new evidence emerged against him, The Associated Press has learned.
The Inzoli case is one of several in which Francis overruled the advice of the Vatican's Congregation for the Doctrine of the Faith and reduced a sentence that called for the priest to be defrocked, two canon lawyers and a church official told AP.
In some cases, the priests or their high-ranking friends appealed to Francis for clemency by citing the pope's own words about mercy in their petitions, the church official said, speaking on condition of anonymity because the proceedings are confidential.
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"With all this emphasis on mercy ... He is creating the environment for such initiatives," the church official said, adding that clemency petitions were rarely granted by Pope Benedict XVI, who launched a tough crackdown during his 2005-2013 papacy and defrocked some 800 priests who raped and molested children.
One is the head of the section and will be replaced before leaving March 31. Vatican spokesman Greg Burke said the others too will be replaced and that staffing in the office, which has a yearslong backlog of cases, would be strengthened after Francis recently approved hiring more officials.
"The speed with which cases are handled is a serious matter and the Holy Father continues to encourage improvements in this area," Burke told AP.
Burke said Francis' emphasis on mercy applied to "even those who are guilty of heinous crimes." He said priests who abuse are permanently removed from ministry, but are not necessarily dismissed from the clerical state, the church term for laicization or defrocking.