Prosecutors in Brussels said that the action, involving dozens of officers and investigators, followed a string of accusations "denouncing abuse of minors committed by a certain number of church figures".
Hundreds of submissions to a special commission set up with the backing of the church in eastern Louvain to examine complaints received of past child abuse were taken away by officers on Thursday.
Police returned to the archdiocese with two more lorries early evening to cart off further material for forensics to comb through seeking hard evidence.
Tarcisio Bertone, from the Vatican secretariat of state, expressed regret on Friday over the "violation of confidentiality of precisely those victims for whom the raids were carried out".
The Vatican statement said it "firmly condemns any sinful and criminal act of minor abuse by members of the church".
Police also seized computer files on Thursday at the home of Godfried Danneels, the former archbishop of Mechelen-Brussels.
A spokesman for Danneels, who led the country's Catholic church for two decades until the turn of the year, said police confiscated a computer from his home before he was escorted to the archdiocese's palace.
Armed police with dogs sealed off the residence, just north of Brussels, "in order to establish if these accusations are backed up or not," Jean-Marc Meilleur, a spokesman for Brussels prosecutors, said.
The Roman Catholic church in Belgium has endured some of the worst of the worldwide paedophilia scandal to beset the Vatican.
|Danneels has denied being involved in any cover-up [EPA]
In April, its longest-serving bishop, Roger Vangheluwe, 73, resigned from his Bruges post after admitting sexually abusing a boy for years.
According to Dirk Deville, a retired priest, hundreds of cases of sexual abuse had been signalled to Danneels going back to the 1990s, but Danneels himself recently denied being involved in any cover-up.
"I cannot recall such a conversation and it would astonish me if I had paid no attention to such a message or had forgotten it," Danneels, a former Belgian primate, insisted.
A victim of a paedophile priest in Wallonia has also accused Andre-Joseph Leonard, Danneels' successor as leader of Belgium's Catholics, of covering up an abuser and keeping him for five years at his post.
Eric De Beukelaer, Leonard's spokesman, recently said: "We did as much as we could at the time, removing the priest involved from all of the pastoral functions that would have put him in contact with children."
In a bid to restore confidence within an increasingly sceptical flock, Belgium's bishops came together in May to publicly beg forgiveness from victims both for the actions of paedophile priests and for the church's "silence" down the years.
Paedophile priest scandals and allegations of high-level cover-ups have surged again since last year across Europe, the US and Brazil.
Earlier this month, Pope Benedict XVI, who has met with abuse victims in Australia, the US and Malta, begged for forgiveness over the matter.
"We ... insistently beg forgiveness from God and from the persons involved, while promising to do everything possible to ensure that such abuse will never occur again," he said.
The pope himself has faced allegations that, as archbishop of Munich and later as the Vatican's chief morals enforcer, he helped to protect predator priests.