He made no mention of the scandal in his Palm Sunday homily, but one of the prayers was "for the young and for those charged with educating them and protecting them".
This year the most solemn week on the Catholic Church's calendar has been stained by a clerical abuse scandal that has spread across Europe to the Pope's native Germany.
And last night it emerged another parish priest in Northern Ireland had taken leave over child safety issues.
Cardinal Sean Brady said this was to allow the civil authorities, which had already been informed, to investigate the matter. But he emphasised that the priest continued to enjoy the right to the presumption of innocence while the matters were being investigated. The parish has not been identified.
Protesters gathered outside the main Catholic church in the UK to call for the Pope's resignation.
With placards stating "Pope Protects Paedophile Priests – Resign!" and "Sex Abuse Cover Up – Pope Must Resign" demonstrators confronted the congregation as it left Westminster Cathedral in central London.
They claim that Pope Benedict XVI was complicit in protecting priests accused of child sex abuse from prosecution.
As such many object to the pontiff's planned state visit to the UK in September.
Human rights campaigner Peter Tatchell was among the demonstrators and said that the Pope "bears personal responsibility for the cover up".
Last week, the Pontiff apologised to victims of child sex abuse in Ireland, but many believe that more could have been done to prevent abuse and report those responsible.
The Pope himself has been subjected to increased scrutiny over how he dealt with sex abuse cases in the past.
As Cardinal Joseph Ratzinger he was involved in the decision to send the Rev Peter Hullermann, accused of abusing boys, to Munich for therapy. He was allowed to return to pastoral duties days later. Hullermann was eventually convicted in 1986.
The church has insisted the then Cardinal Ratzinger was unaware of the decision to allow Hullerman to return to work.
But the New York Times reported on Friday that he was included on a memo stating that this would be the case.
The Pope also stands accused of intervening to halt a church trial of Father Lawrence Murphy, an American priest alleged to have abused up to 200 deaf boys between 1950 and 1975.
Cardinal Ratzinger was head of the Congregation for the Doctrine of the Faith that told bishops in Wisconsin to halt a 1997 trial of Murphy.
The Vatican has defended this decision of the grounds that Murphy – who died a year later – was of an advanced age and that the abuse dated back decades.
But protesters said the cases show up the Pope's failings when it comes to reporting abusers.
During his homily yesterday, the Pope directed himself to young people, as Palm Sunday is traditionally dedicated to the young.
The Vatican spokesman, the Rev Federico Lombardi, has acknowledged that the way the church responded to abuse was "crucial for its moral credibility".
He noted that most of the cases occurred decades ago. "But recognising them, and making amends to the victims, is the price of re-establishing justice and 'purifying memories' that will let us look with renewed commitment together with humility and trust in the future," he said on Vatican Radio.
Separately, a retired Italian cardinal and one-time candidate for the papacy said celibacy for priests should be reconsidered.