“I prayed, but not out of panic,” recalled Mr. Beukelaer, who like others was held in detention and asked to turn over his cellphone and diary. “Others said the Rosary or read the Bible. We didn’t do anything in a collective way because we didn’t want to convey to the staff that this was the end of the world.”

Four days after a coordinated series of raids — also targeting a retired cardinal’s home and the offices of a church commission on sex abuse — the Vatican’s ire is resolute and questions remain about why Belgium, a predominantly Catholic country, decided to be so tough with a type of raid that the Vatican said had never occurred before.

Interviews with church officials and dissident priests, along with accounts in the Flemish press, indicate that prosecutors acted after a trusted witness provided information that suggested that the church was hiding information from its own internal commission on sexual abuse. But Mr. Beukelaer said they were given little direct information about any hidden documents investigators were seeking.

The four dramatic raids unfolded when the bishops gathered for a routine monthly meeting with an agenda that included discussion about what to do with files of priests denounced before the Belgian church’s special commission on sexual abuse. When the police broke up their meeting, investigators discovered the agenda and quickly started questioning the bishops individually. They asked a papal nuncio — the Vatican’s diplomat, who had diplomatic immunity — to leave an hour later.

The driving force behind the prosecutor’s investigation was a formal declaration from an unidentified witness who had warned the authorities that the church had held back documents from its own commission, which was first started in 2000. More than 475 complaints have been filed with the commission since April, when the bishop of Bruges, Roger Vangheluwe, resigned after admitting he had molested a boy.

During the four raids, the commission’s archives were also seized by the police, who collected two and a half truckloads of documents. On Monday, that prompted the new head of that commission, Peter Adriaenssens, a child psychiatrist, to renounce his position along with other members, complaining that the commission had been used by authorities as “bait.”

Shortly after his announcement, Dr. Adriaenssens spent the afternoon with investigators, who for now are focused on investigating child abuse, but could expand to a novel new area to encompass people who knew children were in peril but failed to protect them.

“You have a part of a case that could be against the ones who committed the crimes and you also could have another part of the case against those who didn’t help someone who was in danger,” said Jean-Marc Meilleur, the spokesman for the prosecutor’s office.

He declined to identify the person who had offered the declaration to the prosecutor’s office or the targets of the investigation.

“We are working on a specific case about a specific declaration,” he said. “We are not starting an inquisition against the church. We are working on a file that has some statements, and we are verifying those statements.”

In the Flemish press in Belgium, Godelieve Halsberghe — the former head of the commission and a retired magistrate who resigned amid complaints that church officials were uncooperative — suggested that she may have prompted the spectacular searches.

She declined to return a telephone call Monday, but in previous statements to the newspaper Het Nieuwsblad, she said she had kept copies of records during her tenure on the commission, from 1998 to 2008, that concerned victims and records of conversations with them and Bishop Cardinal Godfried Danneels, who retired in January and whose home was also searched and computer seized last week.

Ms. Halsberghe went to the prosecutor’s office, according to her interview with a local newspaper, after receiving a telephone call from a man who spoke to her in French and asked about the storage of the records before issuing a warning to beware — not only to guard the records, but to protect herself.

One element is clear from the pattern of the raids and the seizure of documents and computers. Over the next few weeks, investigators will be comparing the records that the commission had to those taken from the church to evaluate whether some cases had remained secret.

Norbert Bethune, a former hospital chaplain in Belgium who clashed with church authorities when he reported accusations that priests had sexually abused patients, said he also believed there were missing records, and he credits Ms. Halsberghe for pressing the authorities to act.

But he said the crypt search was unnecessary, the result of information that both the police and church authorities say was provided by chance by a cathedral worker who mentioned that construction work had been taking place near the crypt.

“The bishops are still in a power position,” Mr. Bethune said. “This will not end quickly.”

Mr. Bethune and a retired priest, Rik Devillé, have both provided documents from victims to the prosecutor’s office in the last 15 days that they have collected over the years. Investigators are focusing on allegations of sexual abuse of children, but Father Devillé said that he had amassed complaints that fall into seven categories, from young women who complain that they were forced to give up for adoption babies fathered by priests, to families in missionary countries that say their children were abused by priests who were shuffled there because of similar Belgian scandals.

“They always accused me of trying to destroy the church,” said Father Devillé, who lives in a rectory outside Brussels. “But it’s not me. They are the ones that are destroying the church.”

In the last few weeks – with interest intensifying in the church sex abuse issue – Joël Devillet, a former altar boy, rushed into print a Flemish translation of his book that describes the devastating impact of being molested by a village priest when he was 8 to 14 years old.

His story had been published in French more than a year earlier, but there was no interest, he said, from Flemish readers until the burst of complaints from victims that followed the bishop’s resignation.

Single and unemployed, he said he had avoided relationships or considering marriage because he did not want his own child to experience what he did.

Mr. Devillet said he had also filed complaints with the commission and civil complaints with local authorities. But he has no interest in confronting the priest he accuses of molesting him.

“I have no desire to talk to him,” he said. “What for?”

If the Belgian bishops are feeling government pressure, the Vatican — which has vigorously denounced the raids — is offering a special honor to the leader of the Belgian church.

On Tuesday, Archbishop Léonard is one of 30 bishops who will receive the palium, a vestment worn by the pope that is conferred as a mark of association with the papacy and its powers.

Elisabetta Povoledo contributed reporting.