The probe will be carried out by four research institutes, the German Bishops' Conference said, with the aim of shedding light on a scandal that has shaken the Church to its foundations.
The Conference's commissioner for investigating abuse cases, the bishop of the western city of Trier, Stephan Ackermann, said the study sought "clarity and transparency about this dark side of our Church".
He told reporters that the attempt to understand the prevalence of sexual abuse of youths by clergy was "for the sake of the victims but also in order to see the mistakes for ourselves and do everything we can to ensure they are not repeated."
The head of the research consortium, Harald Dressing, said the report would take three and a half years to complete and was budgeted at about €1 million.
He said the group aimed to learn whether "specific structures and dynamics" within the Church had fostered sexual abuse.
Dressing added that abuse victims would serve as advisors to the probe, from the development of the inquiry methods to the interpretation of the findings.
The researchers are primarily experts in psychology, criminology and sociology.
Since early 2010 and in common with other countries, Germany has been hit by revelations that hundreds of children were physically and sexually abused in Church institutions.
The Church announced in July 2011 it would open its archives, which date back to the end of World War II, on abuse claims.
But in January 2013, the Bishops' Conference said it had severed ties with criminologists commissioned to research sexual abuse by clergy in a row over the right to publish their findings.
The Vatican announced Saturday that a victim of sexual abuse by priests would sit on a new commission created to root out paedophilia in the Church.