The Roman Catholic church was once again at the centre of a child abuse scandal today when police raided the headquarters of the church hierarchy in Belgium. They carried away computers and hundreds of files, amid rumours that church leaders were continuing to cover up abuse cases despite a public plea for forgiveness last month.

Belgian officers today sealed off and searched the headquarters of the church at Mechelen, north of Brussels, where the Belgian bishops' conference was in session, with the papal nuncio taking part. They also searched the home of Cardinal Godfried Danneels, until last year Belgium's most senior prelate, who enjoys a reputation for being a liberal.

In nearby Leuven, east of Brussels, police also searched the premises of the independent church commission investigating hundreds of cases of alleged molestation by clergymen. They took all 475 files belonging to the commission, prompting bewilderment and panic among investigators and victims of sexual abuse.

"The police have a number of accusations connected with the sexual abuse of children within the church," said Jean-Marc Meilleur, a Brussels police spokesman. "The searches are the result of the investigation we started recently. We are collecting evidence material."

The raids centred on the palace of Archbishop Andre-Joseph Leonard, head of the Catholic church in Belgium, on the ancient town's St Rombout's cathedral, and on the residence of the former head of the church in Belgium, Cardinal Danneels.

The long-running but moribund commission in Leuven was resurrected this year to investigate the torrent of allegations that have surfaced, especially since April when one of the most senior clergymen in Belgium, Archbishop of Bruges, Roger Vangheluwe, resigned after admitting he had been abusing a boy for years.

Police declined to say whether any of the individuals at the centre of today's raids were direct suspects or whether the searches concerned evidence affecting other cases.

The commission of inquiry is well-respected and is led by Peter Adriaenssens, one of Belgium's top child abuse experts, whose office has received hundreds of complaints this year and who has threatened to resign should his work be impeded by the church hierarchy. He emerged as a national figure following the notorious Marc Dutroux paedophilia and murder case in 1996 and runs one of the country's most respected child abuse centres.

He voiced outrage and shock at the police actions, saying he had been given no warning, and would now struggle to deliver a report on clerical sexual abuse he was preparing for October. Adriaenssens was in Amsterdam in the Netherlands on Wednesday when his offices were raided. He said that all files in his investigation, concerning 475 cases, had been taken away by the police.

"All day we've been getting mails and calls from victims in panic," he said. "They agreed that we do a report, but they did not want others to see the material … No one asked us a single question. We have no idea why this happened now."

Adriaenssens suggested that a wave of "paranoia" had developed around the flood of allegations coming to light in recent months in Belgium. "There were rumours that the commission was having secret talks with the bishops. Perhaps the investigating magistrate let himself be led by this paranoia."

He added that the raids had thrown into question whether his commission would be able to continue its work. It was set up years ago but had vegetated until this year when the sexual abuse allegations and revelations spread rapidly across the world. The commission's previous head had complained of a lack of co-operation from the church authorities.

Police sources told the Flemish newspaper De Standaard that the raids were carried out because of suspicions that church leaders were failing to hand over all the necessary materials to the commission of inquiry. That was not confirmed by Adriaenssens.

Last month the Belgian bishops' conference issued a pastoral letter pleading for forgiveness both for the sexual abuse by many clergy and for the cover-ups and "silence" that then followed.

"Through the silence priority was given to the reputation of the church institution or the clergyman over the dignity of the child as victim," said the letter.