Belgian officials say the raid on Thursday followed a string of sexual abuse accusations directed at high-level members of the church.
Stefaan De Clerck, the Belgian justice minister, defended the police and accused the Vatican of overreacting.
"The bishops were treated completely normally during the raid on the archdiocese and it is false to say that they received no food or drink," he said, referring to media reports about their treatment.
Possible legal action
Benedict's criticism follows condemnation from other church officials. Tarcisio Bertone, the Vatican's secretary of state, said the detention of several bishops during the raid was "serious and unbelievable".
In a statement, the Vatican said it would consider legal action if the raid turned out to be what it called a "fishing expedition".
The Belgian church was rocked in April when its longest-serving bishop, 73-year-old Roger Vangheluwe, resigned from his post after admitting sexually abusing a boy for years.
Retired priests have also accused church officials of covering up hundreds of cases of sexual abuse going back more than 15 years.