Cardinal Reinhard Marx, center, bishop of Munich and Freising and head of the German Bishops' Conference, arrives for the opening mass of the bishops' conference in Fulda, Germany, Tuesday, Sept. 25, 2018 where the bishops will discuss a study on sexual abuse in the Catholic church in Germany. (Arne Dedert/dpa via AP)

Fulda - A leading German cardinal has apologised for the "failure" of the Catholic Church to address sexual abuse in Germany and the pain it has caused.

"For too long in this Church abuse has been denied, ignored and hushed up. For this failure and for all the pain I ask for forgiveness," said Reinhard Marx, who is leading a conference of German bishops in the central city of Fulda.

The conference was officially presenting a Church-commissioned report detailing decades of sexual abuse of minors by priests in the country.

"We need the courage and the strength to make a new start, and send new signals so that people believe us again. Many people do not believe us anymore," said Marx earlier. He is chairman of the German Bishops' Conference (DBK), which opened on Monday.

"We are shocked and deeply shaken by what has happened," Marx said.

His words were echoed by Pope Francis, who addressed the wider issue of abuse in the Catholic Church during a trip to Estonia.

Young people are turned off by the Catholic Church because of sex abuse and financial scandals, Francis said.

"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," he added.

Marx spoke in Fulda about the abuse victims, saying they "deserve their rights and justice."

"We have to seek out a dialogue with those affected. It is our duty to look into these dark places, to understand and to bring consequences," he said.

The report into abuse was leaked to Spiegel magazine and Die Zeit newspaper earlier this month ahead of its formal presentation at the conference on Tuesday.

It stated that 1,670 priests - or 4.4 per cent of Catholic clerics - had abused 3,677 people between 1946 and 2014 in Germany.

Most of the victims were underage boys and more than than 50 per cent of the victims were under the age of 13, with one in six cases related to accusations of rape.

Many of the perpetrators had simply been moved to other parishes when the abuse was discovered, without informing the communities. In more than 60 per cent of cases, priests went unpunished.

The lead author, Harald Dressing, said that large parts of the Catholic Church were not willing to be open about the abuse.

The scale of the abuse, and the "way that it was handled by those responsible" had "shocked" the researchers, said Dressing, who works in the Central Institute of Mental Health in Mannheim.

"The results of our study suggest that there were and are structures within the Catholic Church that can abet sexual abuse," he said.

The German Church is being urged to offer compensation to the victims in the wake of the report.

"It is still an open wound," Johannes-Wilhelm Roerig, the government official responsible for questions of child sexual abuse, told broadcaster ZDF earlier on Tuesday.

Given that the abuse is mostly historical, the church should decide on what compensation would be appropriate, he said.