Jewish groups and victims of sex abuse by Catholic priests have condemned the Pope's preacher for comparing criticism of the pontiff to anti-Semitism.
US-based abuse victims' group Snap said the remarks were "morally wrong".
The head of Germany's Central Council of Jews described the Easter sermon as unprecedented "insolence".
The Catholic Church has been rocked by a wave of sex abuse scandals this year. The Vatican said Raniero Cantalamessa's did not represent its official view.
Drawing such parallels could "lead to misunderstandings", spokesman Rev Federico Lombardi told the Associated Press.
'Repulsive and offensive'
However, Fr Cantalamessa's sermon was printed in full on the front page of the Vatican's official newspaper, L'Osservatore Romano
At a Good Friday service in St Peter's Basilica in Rome, the Preacher of the Pontifical Household compared criticism of the Church over abuse allegations to "the collective violence suffered by the Jews".
Fr Cantalamessa said he had been inspired by a letter from a Jewish friend who had been upset by the "attacks" against the Pope.
He then read part of the letter, in which his friend said he was following "with indignation the violent and concentric attacks against the Church, the Pope and all the faithful of the whole world".
"The use of stereotypes and the passing from personal responsibility and guilt to a collective guilt remind me of the more shameful aspects of anti-Semitism," he quoted the letter as saying, as the Pope listened.
The comments swiftly provoked angry reactions both from Jewish groups and those representing abuse victims.
The secretary general of Germany's Central Council of Jews, Stephan Kramer, told the Associated Press news agency the remarks were "repulsive, obscene and most of all offensive towards all abuse victims as well as to all the victims of the Holocaust".
David Goldberg, of the Liberal Jewish Synagogue in London, told the BBC the comparison between criticism of the Pope and anti-Semitism was an inept analogy, but he did not think it was ill-intentioned.
"It rather struck me how out of touch so many people in the Vatican are in terms of either understanding the Jewish psyche or in actually dealing with the outrage that so many people, Catholic or otherwise, throughout the world feel," he said.
A spokesman for the Survivors Network of those Abused by Priests (Snap) said the sermon had been "reckless and irresponsible".
"They're sitting in the papal palace, they're experiencing a little discomfort, and they're going to compare themselves to being rounded up or lined up and sent in cattle cars to Auschwitz?" said Peter Isely. "You cannot be serious."
'Failure to act'
Later, Pope Benedict attended a traditional candlelit Good Friday prayer service at the Colosseum in Rome - the Way of the Cross procession, which commemorates Christ's crucifixion.
In a short homily, he made no reference to the abuse scandals that have rocked the Church in recent weeks, but prayed for divine help for Catholics who carry their own crosses every day of their lives.
Then he blessed the crowd, prompting applause and some shouts of "Long live the Pope".
On Saturday, he is to lead an Easter vigil service in St Peter's and on Sunday he is due to deliver his traditional Urbi et Orbi - "for the city and the world" - message and blessing.
The pontiff has been accused personally of failing to take action against a suspected abuser during his tenure as archbishop of Munich - a claim the Vatican strongly denies.
Critics also say that when he was prefect of the Congregation for the Doctrine of the Faith, which deals with sex abuse cases, he did not act against a US priest who is thought to have abused some 200 deaf boys.
On Friday, the Associated Press reported that the then-Cardinal Joseph Ratzinger had also allowed a case against a priest in Arizona to languish at the Vatican for years, despite repeated pleas from a local bishop for the man to be removed from the priesthood.
Documents showed that in 1990, members of a Church tribunal found that Rev Michael Teta had molested children as far back as the late 1970s, it said.
The panel referred the case to Cardinal Ratzinger. But it took 12 years from the time the future Pope assumed control of the case in a signed letter until Rev Teta was removed from the ministry, it was alleged.
The Catholic Church has been engulfed this year by sex abuse scandals, many dating back decades, in Ireland, Switzerland, the Netherlands, Austria, the Pope's native Germany and the US.
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