The incidents took place at the Domspatzen choir in Regensburg between 1945 and 1992. The choir was run by Emeritus Pope Benedict XVI's elder brother Rev Georg Ratzinger between 1964 and 1994.
The report concluded: "The whole system of education was oriented toward top musical achievements and the choir's success.
"Alongside individual motives, institutional motives - namely, breaking the will of the children with the aim of maximum discipline and dedication - formed the basis for violence."
Allegations emerged in 2010 among a spate of claims concerning Roman Catholic clergy. It led to lawyer Ulrich Weber producing a report on what happened.
It concluded there was a "high degree of plausibility" that 547 boys were victims of physical or sexual abuse or both at the Domspatzen choir.
The document counted 500 cases of physical violence and 67 of sexual violence which were committed by a total of 49 perpetrators.
Rev Ratzinger admitted slapping pupils during his time as leader of the choir, although slapping was a common form of punishment in Germany at the time.
He acknowledged that he had not acted on allegations of physical abuse but said unaware of sexual abuse.
The report also criticised the bishop in charge of the area at the time the allegations surfaced. The current bishop has already announced compensation will be awarded to victims by the end of the year.