VATICAN CITY — Pope Francis has quietly reduced sanctions against a handful of pedophile priests, applying his vision of a merciful church even to its worst offenders in ways that survivors of abuse and some of his own advisers question.

In one case, 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 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 said.

Instead, the priests were sentenced to penalties including a lifetime of penance and prayer and removal from public ministry.

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.

‘‘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.

At the same time, Francis also ordered three longtime staffers at the congregation dismissed, two of whom worked for the discipline section that handles sex abuse cases, the lawyers and church official said.

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 said.

He also dispelled rumors that sex-abuse cases would no longer be handled by the congregation, saying the strengthened office would handle all cases submitted.

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.

St. John Paul II was long criticized for failing to respond to the abuse crisis, but ultimately he said in 2002 that ‘‘there is no place in the priesthood or religious life’’ for anyone who would harm the young.

Francis has repeatedly proclaimed ‘‘zero tolerance’’ for abusive priests and in December wrote to the world’s bishops committing to take ‘‘all necessary measures’’ to protect them.

But he also recently said he believed sex abusers suffer from a ‘‘disease’’ — a term used by defense lawyers to seek mitigating factors in canonical sentences.

Marie Collins, an Irish abuse survivor and founding member of Francis’ sex-abuse advisory commission, expressed dismay that the congregation’s recommended penalties were being weakened and said abusers are never so sick that they don’t know what they’re doing.

‘‘All who abuse have made a conscious decision to do so,’’ Collins said. ‘‘Even those who are pedophiles, experts will tell you, are still responsible for their actions. They can resist their inclinations.’’

Victim advocates have long questioned whether Francis is committed to continuing Benedict’s tough line, given that he had no experience dealing with abusive priests or their victims in his native Argentina.

While Francis counts Cardinal Sean O’Malley of Boston as his top adviser on abuse, he has also surrounded himself with cardinal advisers who mishandled abuse cases in their archdioceses.

The church official who confirmed the clemency decisions stressed that to his knowledge, none of Francis’ reduced sentences had put children at risk.

Many canon lawyers and church authorities argue that defrocking pedophiles can put society at greater risk because the church no longer exerts any control over them. They argue that keeping the men in restricted ministry, away from children, at least enables superiors to exert some degree of supervision.

But Collins said the church must also take into account the message that reduced canonical sentences sends to both survivors and abusers.

‘‘While mercy is important, justice for all parties is equally important,’’ Collins said in an e-mail. ‘‘If there is seen to be any weakness about proper penalties, then it might well send the wrong message to those who would abuse.’’

It can also come back to embarrass the church. Inzoli, a well-connected Italian priest, was found guilty by the Vatican in 2012 of abusing boys and ordered defrocked. He appealed and in 2014 Francis reduced the penalty to a lifetime of prayer, prohibiting him from celebrating Mass in public or being near children, barring him from his diocese and ordering five years of psychotherapy.

In November, an Italian criminal judge showed little mercy in convicting Inzoli of abusing five children, aged 12 to 16, and sentencing him to four years and nine months in prison. The judge said Inzoli had a number of other victims but their cases fell outside the statute of limitations.

Burke said the Vatican recently initiated a new canonical trial against Inzoli based on new information. He declined to elaborate.

Amid questions about how the battle against abuse was faring, Francis recently named O’Malley, who heads his sex-abuse advisory commission, as a member of the Congregation for the Doctrine of the Faith. But it’s not clear what influence he can wield from his home base in Boston.

Francis scrapped the commission’s proposed tribunal for bishops who mishandle abuse cases, after legal objections from the congregation.

The commission’s other major initiative — a guideline template to help dioceses develop policies to fight abuse and safeguard children — is gathering dust. The Vatican never sent the template to bishops’ conferences, as the commission had sought.