Last week, police raided the home of a retired bishop, opened the grave of at least one archbishop and detained Belgium's nine current serving bishops as they met, seizing their mobile phones and only releasing them after nine hours.
Pope Benedict described the raids by officers investigating abuse claims as "surprising and deplorable" and demanded that the church be allowed a role in inquiries into child molesters in its ranks.
In a message to the head of the Belgian bishops' conference, Monsignor André-Joseph Léonard, the pontiff condemned the raids and offered his support to the bishops "in this sad moment".
"I want to express, dear brother in the episcopate, as well as to all the bishops of Belgium, my closeness and solidarity in this moment of sadness, in which, with certain surprising and deplorable methods, searches were carried out," he said.
"I hope that justice will follow its course while guaranteeing the rights of individuals and institutions, respecting the rights of victims, [and] acknowledging those who undertake to collaborate with it."
The Vatican has also protested to Belgium's ambassador to the Holy See. Yesterday, Cardinal Tarcisio Bertone, the Vatican secretary of state, said: "There are no precedents for this, not even under communist regimes."
But the raids were welcomed by the American clerical abuse victims group Snap. "Vatican officials who criticise the Belgian police raid of the Brussels church hierarchy should be ashamed of themselves," said Joelle Casteix of Snap. "While Roman church officials talk about stopping abuse, Belgian police officials take action to stop abuse."
As cases of abuse by priests have emerged throughout Europe this year, the Belgian church has apologised for failing to root out abusers in the past and promised a crackdown.
On Friday, the pope appointed Monsignor Jozef De Kesel as the bishop of Bruges to replace Roger Vangheluwe, 73, who resigned in April over abusing a boy. Vangheluwe was the first European bishop to step down after confessing to abuse.
As part of their investigation into recent claims of abuse, police last week drilled into the tombs of two archbishops at the cathedral in Mechelen, north of Brussels, using cameras to look for hidden documents, a church official said. Investigators said only one tomb had been opened.
Léonard condemned the raid as being inspired by "crime novels and the Da Vinci Code".
Police took documents and a computer from the home of his predecessor, Godfried Danneels, and seized documents from an independent panel investigating 500 cases of suspected abuse by priests.
After initially treating the abuse revelations emerging in Europe as a plot to discredit the church, Vatican officials have increasingly admitted the need for it to co-operate more closely with police.
But in his reaction to the Belgian raids, the pope stressed that abuse within the church needed to be handled by both civil and canon law, "respecting their reciprocal specificity and autonomy".
Avvenire, the newspaper of the Italian Bishops' Conference, went further, claiming the police investigation went "beyond the legitimate requirements of justice" and was the sign of a secular government's "desire to attack the church in its entirety" by a secular government.
SIC: TGUK