Pope Benedict has directly intervened in a row over police raids on church properties in Belgium.
The BBC reports the raids were part of a child sex abuse investigation, which the Pope said he supported.
But he criticised the way they were carried out, and said the autonomy of the Catholic church must be respected.
Several buildings and the graves of two prelates were searched on Thursday in raids targeting a retired archbishop.
The Vatican has summoned the Belgian ambassador to the Holy See to voice its anger at the incident.
The Catholic Church in Belgium has apologised for its silence on abuse cases in the past.
In April, the bishop of Bruges resigned and admitted to sexual abuse before and after becoming a bishop.