Pope Benedict XVI called a recent raid by Belgian police on Catholic properties "surprising and deplorable" in a message delivered on Sunday.
Benedict's message came following last Thursday's raid at the Cathedral of Mechelen and the archbisopric of Mechelen-Brussels, where police confiscated documents and mobile phones and detained bishops in a search for evidence of sexual abuse of minors.
The police also reportedly "violated" some of the tombs in the Cathedral, to which bishops present at the raid expressed "great surprise" and "indignation."
"The dismay felt over those actions, is compounded by regret for some breaches of confidentiality, owed to those very victims for whom the searches were conducted," the bishops said in a statement.
The following Sunday, the Pope expressed "special closeness and solidarity" to the clergy at the Church in Belgium, noting that the bishops who were raided were gathered to discuss the issue of abuse in the church.
Benedict further highlighted how the "serious matters" of sex abuse "should be dealt with by both civil law and canon law, while respecting the specific nature and autonomy of each."
"In this context, I trust that justice may run its course in order to guarantee the fundamental rights of persons and of institutions, at the same time respecting victims, showing unconditional recognition for those who undertake to collaborate, and rejecting everything that obscures the noble goal with which justice is assigned," the Pope said.
Meanwhile, staff of a Belgian Church-backed commission conducting investigations into child abuse in the region resigned over the raids, saying that the commission "had been used as bait," according to BBC.
According to reports, the commission's 475 case files were taken along with personal computers.
During a news conference on Monday, the commission's head, Peter Adriaenssens,expressed "shock" at the raid and his concern for the hundreds of victims who had given the commission "their trust."
"We received e-mails, telephone calls in the past few hours from people who are panicking about what will happen with their private details. Will their parents find out? Will they read their story in the newspapers? Will their spouse, who wasn't really aware, now find out via the media or the justice department?" Adriaenssens said.
The Belgian Church is among the Catholic dioceses that have been shaken by the continuing abuse scandal. In April, the Bishop of Bruges Roger Vangheluwe stepped down after admitting to sexually abusing a young man.