Pope Benedict XVI has also apologised earlier today, to people sexually abused by members of the clergy in Australia.
Pope Benedict XVI has said he was "deeply sorry" for the suffering of people sexually abused by members of the clergy in Australia.
"Here I would like to pause to acknowledge the shame which we have all felt as a result of the sexual abuse of minors by some clergy and religious in this country," Pope Benedict said in his homily.
The pontiff then moved from the original text of his homily to make the apology.
"Indeed I am deeply sorry for the pain and suffering the victims have endured and I assure them that, as their pastor, I too share in their suffering."
He said such abuses were a source of shame and deserving of condemnation, and that the perpetrators must be brought to justice.
He described the "evil" acts as a grave betrayal of trust.
"These misdeeds, which constitute so grave a betrayal of trust, deserve unequivocal condemnation.
"They have caused great pain, they have damaged the church's witness."
The Pope raised the issue before 3,400 people invited to attend the consecration of the altar of St Mary's Cathedral in Sydney, where he has been participating in World Youth Day (WYD) activities.
It had been widely expected the he would make such an apology during his first Australian visit, although the Vatican's head of media earlier this week indicated a Papal apology was not a certainty.
The issue of sex abuse had been prominent in the lead up to the massive Catholic youth festival, with Sydney Archbishop Cardinal George Pell, the leader of the Catholic church in Australia, was forced to defend his handling of a number of historic allegations.
Support groups for victims of church abuse in Australia, whose numbers are not known but who activists say are in the thousands, had demanded the pope make a full and open apology for clergy abuse and do more to prevent future abuse.
The hopes for an apology were boosted after the Pope's visit to the United States in April, where he said he was "deeply ashamed" of sex abuse committed by clergy and pledged he would do whatever was possible "so this cannot happen again in the future".
Fr Anthony Robbie, a lecturer in church history and theology, said the Pope went further on Saturday than he had in the US.
"I would say it is stronger than the words that he used in the United States," he told Sky News.
On Saturday, Pope Benedict said it was time to work together in "combating this evil".
"Victims should receive compassion and care, and those responsible for these evils must be brought to justice," he said.
"It is an urgent priority to promote a safer and more wholesome environment, especially for young people.
"In these days marked by the celebration of World Youth Day, we are reminded of how precious a treasure has been entrusted to us in our young people, and how great a part of the church's mission in this country has been dedicated to their education and care.
"As the church in Australia continues, in the spirit of the gospel, to address effectively this serious pastoral challenge, I join you in praying that this time of purification will bring about healing, reconciliation and ever-greater fidelity to the moral demands of the gospel."
Fr Brian Lucas, general secretary of the Australian Bishops Conference, said he hoped the Pope's words spurred an ending to the suffering of victims.
"We have to bring this great tragedy to an end. We have to be so conscious of the suffering of so many people and this has been a time of great suffering for those victims," he told Sky News.
"And the church, through the person of the Holy Father, in a very unequivocal way this morning has made acknowledgment of that."
Meanwhile, a man whose daughters were raped by a Melbourne priest says the Pope's apology to abuse victims is disappointing in that it offers no practical help to those who have suffered.
Anthony Foster and his wife Christine this week cut short a UK holiday and flew to Sydney in the hope of securing an audience with the Pope or Sydney Archbishop Cardinal George Pell.
Melbourne priest Kevin O'Donnell raped the couple's two daughters, Emma and Katherine, when they were in primary school.
O'Donnell died in prison about 10 years ago, and the Fosters have accused the Catholic church of stalling their compensation claim, which was eventually settled out of court after an eight-year legal battle.
Emma Foster committed suicide this year at the age of 26, while her sister Katherine drank heavily and was left disabled when she was hit by a drunk driver in 1999.
Mr Foster said the papal apology was disappointing.
"Our first reaction is disappointment," Mr Foster told AAP.
"They are only words - the same thing we've been hearing for 13 years.
"It is simply an apology, there is nothing practical there which is what we were looking for.
"The Pope apologised in the past to America, and what we are very concerned about is the lack of practical help for the victims.
"This is a first step that had been taken long ago."