"It is understandable that you find it hard to forgive or be reconciled with the church," he said.
"In her name, I openly express the shame and remorse that we all feel."
'Acknowledge your guilt'
Benedict used his harshest words for the abusers themselves, saying they had betrayed the trust of the faithful, brought shame on the church and now must answer before God and civil authorities.
"Conceal nothing," he told them. "Openly acknowlege your guilt, submit yourselves to the demands of justice, but do not despair of God's mercy."
Benedict faulted their superiors, the Irish bishops, for having failed "sometimes grievously" to apply the church's own law which calls for harsh punishments for child abusers, including defrocking them.
But he did not rebuke them specifically for having failed to report cases of abuse to police, saying only that serious mistakes were made and that now they must "continue to co-operate with civil authorities".
Laurence Lee, Al Jazeera's correspondent in Dublin, said victims of abuse will see the letter as a massive let down.
"The concrete initiatives that the pope suggested should be carried out involved things like Friday penances, fasting, works of mercy and reading the scriptures," he said.
"... clearly what the victims of abuse and pressure groups ... want are concrete measures which are much more to do with resignations or even criminal charges against bishops and priests.
"It was more a re-statement of the importance of the laws of the church which historically have been seen by the church as more important than an overriding criminal law."
Letter 'falls short'
One in Four, a victims' rights group, said that it was deeply disappointed by the letter.
"We feel the letter falls far short of addressing the concerns of the victims," Maeve Lewis, the executive director of the group, said.
The Netherlands: 200 cases of sexual abuse being investigated
Switzerland: 60 cases being investigated
Germany: 300 reported cases of sexual abuse
She said the pope's letter focused too narrowly on lower-ranked Irish priests without recognising the responsibility of the Vatican.
While not punishing those in the upper echelons of the church who covered up the allegations of abuse, it does begin an investigation into the actions of specific dioceses, seminaries and religious orders.
Three Irish government-ordered investigations published from 2005 to 2009 have documented how thousands of Irish children suffered rape, molestation and other abuse by priests in their parishes and by nuns and brothers in boarding schools and orphanages.
Irish bishops did not report a single case to police until 1996 after victims began to sue the church.
In the last week, Cardinal Sean Brady, Ireland's senior churchman, has come under fire after it emerged he swore two children to secrecy during a 1975 probe into their abuse by one priest, Father Brendan Smyth.
The Irish investigations have faulted Rome for sending confusing messages to the Irish church about norms to be followed and, in general, for what it called the absence of a incoherent set of canon laws and rules to apply in cases of abuse.
Benedict's letter addressed only the scandal in Ireland, not the other cases of abuse which have recently come to light in other countries across Europe, including in the pope's native Germany.
Greg Watts, the author of a biography of Pope Benedict XIV, said he expected more cases of abuse to surface in the future.
"What's happened in Ireland has happened in many countries," he told Al Jazeera on Saturday.
"I think there will be more revelations to come out form Poland and elsewhere because this type of thing is not unique to a particular country or culture.
"But I am dismayed by the church's inability to deal with this ... What we really need is reform of the government of the church. I think a lot of these problems that we've had is down to a secrecy among the bishops."
Benedict, who served as archbishop of Munich from 1977 to 1982, has yet to speak about the hundreds of abuse cases emerging since January in Germany.
These include the Reverend Peter Hullermann, who was already suspected of abusing boys in the western German city of Essen when Ratzinger approved his transfer to Munich for treatment in 1980.