He said Catholics were "under attack from the world which talks to us of our sins" and should see the necessity "to recognise what is wrong in our lives".
In was the Pope's first reference to the abuse scandal for nearly a month.
Later, German bishops said they would revise their abuse guidelines to bring in prosecutors early to investigate.
Justice Minister Sabine Leutheusser-Schnarrenberger earlier told the head of the German Bishops Conference, Archbishop Robert Zollitsch, that internal church investigations must not hinder prosecutors' work.
The existing guidelines dating back to 2002 state that accused priests are advised to contact the authorities on their own in "proven cases" of abuse, and that Church leaders are not required to do so.
On Monday, the Vatican published what it said was a long-standing Church policy telling bishops that they should report abuse cases to police. But critics said the move was an attempt to rewrite history.
Penance 'a grace'
Speaking during a homily at a private mass at the Vatican on Thursday, Pope Benedict appeared to make his first reference to the issue since 20 March, when he sent a letter to the Irish people about the abuse scandal in their country.
"I must say, we Christians, even in recent times, have often avoided the word 'repent', which seemed too tough," he said.
"But now, under attack from the world which talks to us of our sins, we can see that being able to do penance is a grace and we see how necessary it is to do penance and thus recognise what is wrong in our lives."
The Pope said this involved "opening oneself up to forgiveness, preparing oneself for forgiveness, allowing oneself to be transformed".
The BBC's David Willey in Rome says the words were generic, but his meaning was clear - the gravity of the scandal harms all Christians.
Pope Benedict also used the opportunity to hit back at critics of the Church, portraying them as in the thrall of a conformist dictatorship.
"Conformism which makes it obligatory to think and act like everyone else, and the subtle - or not so subtle - aggression towards the Church, demonstrate how this conformism can really be a true dictatorship," he said.
'Unjust attacks'
On Monday, the Vatican's Secretary of State, Cardinal Tarcisio Bertone, outraged gay rights groups worldwide saying it was homosexuality - not the Church's celibacy - which lay behind the abuse of minors.
The Vatican sought to "clarify" the remarks on Wednesday, saying the Church was not trying to make assertions of a "psychological or medical nature".
Earlier this month, the Pope's personal preacher was forced to apologise for having highlighted a comparison between criticism of the Church over the abuse allegations and "the collective violence suffered by the Jews".
Meanwhile, the cardinal who oversees the Church's 400,000 priests, has urged them to gather in St Peter's Square in June to show the Pope their "determined rejection of the unjust attacks of which he is a victim".
Cardinal Claudio Hummes, the prefect of the Congregation of the Clergy, wrote to priests calling on them to show "our solidarity, our support, our confidence, and our unconditional communion".
The Pope, who celebrates his 83rd birthday on Friday, is due to visit the Mediterranean island of Malta this weekend.
A Vatican spokesman has indicated that he may have a discreet private meeting with victims of clerical abuse, some of whom have asked to meet him, but this has not been confirmed.
There has been a high incidence of reported cases of abuse in Malta, whose inhabitants are mainly Catholic, our correspondent says.
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SIC: BBC