In his Palm Sunday address the Pope said that Jesus Christ "leads us towards courage which does not allow us to be intimidated by the chatter of dominant opinions, towards patience which supports and sustains others".
The pontiff did not refer to accusations over his handling of cases of paedophile priests, both as Archbishop of Munich from 1977 to 1982 and subsequently as head of doctrine at the Vatican.
However, Vatican watchers said his meaning today was clear "in the current context".
One Palm Sunday prayer, recited in Portuguese during the Mass, referred to "the young and for those charged with educating them and protecting them."
Palm Sunday commemorates Jesus Christ's triumphant entry into Jerusalem, and is the start of the Church's Holy Week, which includes Good Friday, the sombre day of Christ's Crucifixion, and Easter Sunday, which marks Jesus' resurrection.
It has been overshadowed by the clerical abuse scandal which has spread across Europe to the Pope's native Germany.
On Good Friday 2005, shortly before the death of John Paul II and Pope Benedict's election as his successor, the future Pope - then Cardinal Joseph Ratzinger - condemned the "filth" in the Church, a reference to paedophilia scandals.
Vatican officials maintain he has since been active in combating clerical sex abuse, especially during his visit to the United States in 2008, when he met a number of victims. In his recent pastoral letter to Irish bishops he called sex abuse a "grave sin" and a "heinous crime".
However the Vatican is on the defensive and bracing for further revelations. It has already emerged that as Cardinal Ratzinger, the Pope allowed Father Peter Hullermann, a known paedophile priest, to receive "therapy" in his Munich diocese in 1980.
Father Hullermann was later allowed to resume pastoral work with children, and in 1986 was convicted of abusing minors.
In addition a case has come to light in which the Congregation for the Doctrine of the Faith told Wisconsin bishops to halt a church trial for Father Lawrence Murphy, a priest alleged to have abused up to 200 deaf boys, at a time when Cardinal Ratzinger was head of the Congregation.
The Vatican insists Ratzinger was unaware of Father Hullermann's return to pastoral work and has also defended his handling of the Wisconsin case, saying Father Murphy was in ill health and the accusations against him dated back decades. He died not long after the Church trial against him was dropped.
In his homily today the Pope addressed himself to young people, reminding them that "Christian life is a path, or pilgrimage with Christ, a walk in the direction that he has chosen and shows us."
On Saturday, the Vatican spokesman, Father Federico Lombardi, acknowledged that the way the Church responds to the abuse scandal will be "crucial for its moral credibility."
He noted that most of the cases that have come to light recently occurred decades ago, adding "But recognising them, and making amends to the victims, is the price of re-establishing justice and purifying memories that will let us look ahead with renewed commitment together, with humility and trust in the future".
Monsignor Robert Zollitsch, head of the German bishops' conference, has said the Vatican is compiling information from around the world with the aim of setting out new guidelines on abuse.
Cardinal Carlo Maria Martini, former archbishop of Milan and at one time a contender for the papacy, today Sunday told an Austrian paper that priestly celibacy should be "reviewed" as a possible cause of abuse by clergy.
The Vatican has rejected suggestions that celibacy causes abuse, and Pope Benedict this month reaffirmed it as "a gift to God".
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