Pope Benedict XVI says the Church’s child abuse scandal shows that the greatest threat to Catholicism comes from “sin within” the Church.
He made his comments in response to a question while en route to Portugal.
Critics have previously accused the Vatican of attempting to blame the media and the Church’s opponents for the escalation of the scandal.
But the Pope made clear its origin came from within the Church itself, and said forgiveness “does not replace justice”.
‘Need for penance’
“Today we see in a truly terrifying way that the greatest persecution of the Church does not come from outside enemies, but is born of sin within the Church,” the pontiff told reporters on a plane bound for Portugal.
His comments were his most direct response to press questions, and some of his strongest words yet on the abuse scandal, says the BBC’s Vatican Correspondent, who is travelling with the Pope.
Benedict said the Church has “a very deep need” to acknowledge that it must do penance for its sins and “accept purification”.
However, he added that forgiveness should not be a substitute for justice.
There has been a wave of allegations in the past few months that Church authorities in Europe and North and South America failed to deal properly with priests accused of child sex abuse, sometimes just moving them to new parishes where more children were put at risk.
The Pope himself has been accused of being part of a culture of secrecy, and of not taking strong enough steps against paedophiles when he had that responsibility as a cardinal in Rome.
However, his supporters say he has been the most pro-active pope yet in confronting abuse.
The Pope later landed at Lisbon, the capital, despite fears that the volcanic ash cloud affecting flights in the region would disrupt his plans.
During the four-day trip he is due to celebrate open-air Masses in Lisbon, as well as at the Catholic shrine of Fatima, and in Oporto.
Church officials say he will address Europe’s spiritual and economic crisis.
Although nearly 90% of people in Portugal are reported to be Catholics, only about 20% attend Mass regularly, the BBC’s Vatican correspondent, David Willey, reports from Lisbon.
Pope Benedict intends to tell the Portuguese to seek solace in their faith to relieve the gloom of financial hardship, he says.
Carlos Azevedo, the auxiliary bishop of Lisbon and the co-ordinator of the papal visit, said on Monday that the pontiff will speak about “the joy of faith and hope”.
“The moral values guiding the economy and politics show that there is a spiritual crisis,” he said.
Portugal has been one of the countries worst affected by the economic problems troubling many European states.
Tens of thousands of people are expected at the Mass in Lisbon on Tuesday.
But the highlight of the trip is a visit to Fatima on Wednesday and Thursday, where a giant outdoor Mass has been planned for as many as 500,000 people.
Fatima is one of the main sites of Christian pilgrimage in Europe.
The Pope will be marking the anniversary of the day in 1917 when three Portuguese shepherd children reported having visions of the Virgin Mary in Fatima.