By describing the decades of child abuse in Catholic parishes, schools and church-run institutions and parishes in Ireland as a "mystery", the pontiff could further anger rank-and-file faithful in Ireland.
Benedict commented on the scandals of sexual abuse and cover-ups by church hierarchy in a pre-recorded video message for an outdoor Mass attended by 75 000 Catholics, many from overseas, in Ireland's largest sports stadium.
Ireland's prime minister and president attended the Mass, the final event of a Eucharistic Congress aimed at shoring up flagging faith.
The weeklong Eucharistic Congress, held by the Vatican every four years in a different part of the world, took place against a backdrop of deep anger over child abuse cover-ups and surveys showing declining weekly Mass attendance in Ireland, where church and state were once tightly entwined.
"How are we to explain the fact that people who regularly received the Lord's body and confessed their sins in the sacrament of Penance have offended in this way?" said the pope, referring to church staff who abused children.
Fight for survival
"It remains a mystery," he said. "Yet evidently their Christianity was no longer nourished by joyful encounter with Jesus Christ. It had become merely a matter of habit."
Dublin Archbishop Diarmuid Martin has said the church in Ireland is facing a grave fight for survival.
"Your forbears in the church in Ireland knew how to strive for holiness and constancy in their personal lives," Benedict said in his message.
In a reference to the Vatican's insistence on Sunday Mass attendance, Benedict said Catholic faith "is a legacy that is surely perfected and nourished" at Mass.
Yet, he said, "thankfulness and joy at such a great history of faith and love have recently been shaken in an appalling way by the revelation of sins committed by priests and consecrated persons against people entrusted to their care".
"Instead of showing them the path towards Christ, toward God, instead of bearing witness to his goodness, they abused people and undermined the credibility of the church's message," the pope said.
For more than a decade, advocates for those abused by clergy have been demanding that church leaders in Ireland and at the Vatican accept blame for protecting paedophile priests.
Four state-ordered investigations have documented how tens of thousands of children from the 1940s to the 1990s suffered sexual, physical and mental abuse at the hands of priests, nuns and church staff in three Irish dioceses and in a network of workhouse-style residential schools.
In Ireland, the United States and many other countries, bishops and other church leaders have been accused of systematically covering up paedophile priests, often by shuffling them from parish to parish without telling the faithful about the abuse.
Benedict's evoking "mystery" disappointed the victims' advocacy group Snap, or Survivors Network of those Abused by Priests. A Snap official, Barbara Dorris, said the pope was speaking in "platitudes, refusing to even accurately name the crisis".
"The pontiff's wrong: There's little mystery here," said Dorris in an e-mailed statement.
She cited priests' having "sometimes almost absolute power, over devout and defenceless kids", as well as bishops who abuse power and "ignore, hide and enable heinous crimes against kids".