The flames of fury over priest sex abuse scandals are eroding the faith of Catholics and chasing many from pews, Pope Francis admitted Tuesday – and the church needs "to change."

The pope's frank comments, delivered before young people in Estonia on the final day of his pilgrimage to the Baltics, coincided with a stinging report of abuse of children by Catholic clergy in Germany.

Francis told the youths the church must take action to restore the faith of future generations and be transparent and honest.

“They are outraged by sexual and economic scandals that do not meet with clear condemnation, by our unpreparedness to really appreciate the lives and sensibilities of the young, and simply by the passive role we assign them,” he said at the Kaarli Lutheran Church in the Estonian capital of Tallinn.

“We ourselves need to be converted,” he said. “We have to realize that, in order to stand by your side, we need to change many situations that, in the end, put you off.”

The pope's public admission about the toll of the abuse scandals came as anger over priest sex abuse has reached fever pitch.

The Vatican was assailed for not responding immediately to the release of a grand jury report in August by the Pennsylvania attorney general alleging that church leaders protected more than 300 "predator priests" in six Roman Catholic dioceses across the state for decades. The report claimed the church was more interested in protecting its own interests and the abusers than tending to the victims.

After two days of silence, the Vatican condemned the incidents as "criminal and morally reprehensible.”

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There have been charges of a cover-up of the scandals that have placed the pope's personal handling of the issue in a harsh spotlight. A retired Vatican ambassador, Archbishop Carlo Maria Vigano, who alleged earlier this month that Francis hid sex abuse allegations against U.S. Cardinal Theodore McCarrick, has even called on the pope to resign.

Some Vatican observers have argued the latest allegations are part of a fierce battle over the future direction of the Catholic church, with conservatives who oppose the pope and progressives backing Francis' efforts to bring some changes.

Read:'Civil war' divides world's Catholics amid allegations of sex abuse, cover-up

The priest abuse scandal, which erupted in Ireland in the 1990s, has had global reach, rocking countries from Argentina to Australia.

A report from a German bishops conference released Tuesday found that 3,677 people – more than half of them 13 or younger and nearly a third of them altar boys – were abused by clergy from 1946 to 2014.

Justice Minister Katarina Barley said the report was "probably only the tip of the iceberg," according to the Guardian.

The report found damning evidence: Files were manipulated or destroyed, abusers were moved to other dioceses, cases were not brought to justice.

There have been signs Francis is trying to take greater control of the issue. Earlier this month, he summoned the presidents of Catholic bishops conferences worldwide to the Vatican in February to discuss protecting children and preventing sexual abuse by priests.

The meeting, on Feb. 21-24, is believed to be the first of its kind.

Contributing: John Bacon, USA TODAY, The Associated Press