News magazine Der Spiegel said bishops have decided to allow the Criminological Research Institute of Lower Saxony (KFN) to access files from all 27 dioceses dating back 10 years.
In nine of those bishoprics, researchers will be granted access to files from the year 1945 onward.
Following a wave of revelations involving sexual abuse by Catholic clergy and staff, the Church is looking to repair its image and win back credibility. The move marks a sudden reversal of longstanding Church policy, whereby investigations into abuse cases have been handled internally.
German Justice Minister Sabine Leutheusser-Schnarrenberger had previously appealed to the Church to engage state prosecutors in the investigations, but those calls went unheeded.
Der Spiegel said Catholic bishops attending the German Bishops' Conference on June 20, adopted a resolution allowing KFN access to the Church's files. A team from the research institute would oversee Church staff in reviewing the documents for any indications of sexual abuse violations.
Researchers from KFN would then evaluate any files that had been flagged.
The Church also plans to ask abuse victims to fill out a questionnaire and will request interviews from victims and perpetrators.
Church bishops hope that information will shed light on the circumstances of the violations, how they were dealt with internally, and how the findings might help prevent future cases of abuse.
But the team could have their work cut out for them, as past investigations into abuse in Church-run institutions have indicated that some violations were brushed under the rug.
Der Spiegel said attorney Marion Westphal reached a similar conclusion while investigating abuse cases in the Munich and Freising dioceses between 1945 and 2009.
"We're looking at the large-scale destruction of files here," she said.