"If -and it was not my intention to do so - I hurt the sensitivities of Jews and victims of paedophilia, I am truly sorry and I ask for forgiveness," Fr Raniero Cantalamessa said in an interview with Italy's Corriere della Sera newspaper.
He also said the pope was not aware of his remarks and that the pontiff heard them for the first time along with everyone else in St. Peter's Basilica on Good Friday.
"Not only did the pope not inspire me but, like everyone else, heard my words for the first time like everyone else during the liturgy in the basilica," he said.
Fr Cantalamessa, speaking with the pope sitting nearby, said Jews throughout history had been the victims of "collective violence" and drew comparisons between Jewish suffering and attacks on the Church.
"The use of stereotypes, the shifting of personal responsibility and guilt to a collective guilt remind me of the most shameful aspects of anti-Semitism," Fr Cantalamessa quoted from a letter he said he had received from a Jewish friend.
A Vatican spokesman later said the comparison "is absolutely not the line of the Vatican and of the Catholic Church".
Jewish groups around the world have reacted with shock to the comments, using words like repugnant, obscene, and offensive to describe the sermon.
Rome's chief rabbi, Riccardo Di Segni said the remarks were particularly insensitive because they were made on the day that for centuries Christians prayed for the conversion of the Jews, who were once held collectively responsible for Jesus' death.
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