Reuters has reported that the case was brought by a man, Joel Devillet, who claimed he was abused by a priest when he was a 14-year-old choir boy in the late 1980s.
Mr Devillet later become a priest himself and told the Church of his experience of abuse. However it did not alert authorities, the court heard on Thursday.
The court said: "At no moment at the church court was Joel Devillet recognised as a victim."
It added that Archbishop Leonard bore some blame: "The way in which Bishop Leonard treated the case of Joel Devillet constituted misconduct."
Leonard has been criticised in the past for saying it is vengeful to prosecute retired priests, and that the Church does not need to compensate victims.
A report published in 2010 found child abuse was widespread in the Belgian Church, and had driven at least 13 victims to suicide.
A high profile case came out the same year, when the Bishop of Bruges resigned after admitting he had sexually abused a nephew.
The Archbishop's lawyer, Philippe Malherbe, said the Archbishop did not agree with the court's judgement but had not yet made up his mind whether he will appeal the result.
He said: "The court lists various things that certain people should have done, but nothing that Monsignor Leonard categorically should have done. That nuance is important."