Pope Benedict told Irish bishops gathered at the Vatican that wounds caused by sexual abuse in the Catholic Church in Ireland "run deep."
He instructed the bishops to do whatever necessary to prevent repeat offences and rebuild confidence in the clergy.
"In the exercise of your pastoral ministry, you have had to respond in recent years to many heart-rending cases of sexual abuse of minors," the Pope told the bishops who are in Rome as part of the ad limina visit by the Irish Bishops' Conference to the Vatican.
"The wounds caused by such acts run deep, and it is an urgent task to rebuild confidence and trust where these have been damaged."
The Pope, in rare comments about the sensitive issue, said the Church needed to establish the truth about abuses and ensure that "the principles of justice are fully respected".
"It is important to establish the truth of what happened in the past, to take whatever steps are necessary to prevent it from occurring again," the Pope said, according to a copy of the speech released by the Vatican.
"Above all, (it is important) to bring healing to the victims and to all those affected by these egregious crimes.
The Pope said such crimes should be seen as exceptions in Ireland.
"The fine work and selfless dedication of the great majority of priests and religious in Ireland should not be obscured by the transgressions of some of their brethren," he said.
"I am certain that the people understand this, and continue to regard their clergy with affection and esteem."
In May, the Pope took his first major decision involving sexual abuse charges since his election last year. He disciplined the ageing Mexican founder of an influential Catholic religious order who was accused of sexual abuse, instructing him to retire to a life of "prayer and penitence".
Archbishop Seán Brady invited the Pope to Ireland. However, Pope Benedict did not refer to the invitation during his own address.