Many of the 5,000 documents about suspect priests in the Dublin archdiocese were among those sought by the Garda National Bureau of Criminal Investigations which investigated clerical abuse in the archdiocese in 2003.
That investigation was launched in the wake of a documentary exposing the Church's failure to act on complaints from victims.
However, gardai had to negotiate with Cardinal Connell's office over accessing confidential church files on suspect priests, according to sources on the investigation.
Gardai could have obtained a search warrant to seize the files but agreed instead to limited, supervised access.
Detectives were allowed to view the files on priests in the diocesan office under the supervision of the Church officials, according to garda sources. They were not allowed to remove the file.
Despite the restricted access, garda sources said they were happy with the Church's co-operation.
The probe resulted in a number of additional charges being brought against known abusers.
The same files are now at the centre of last week's dramatic High Court showdown between Cardinal Connell and his successor, Archbishop Diarmuid Martin.
Cardinal Connell sought to stop the release of 5,000 documents to the Commission investigating clerical sex abuse in the archdiocese, on the basis that they contained legal advice to him which was privileged.
A full hearing on whether the documents are governed by confidentiality will be heard in the High Court tomorrow.
Cardinal Connell's legal challenge reflects growing unease within some quarters of the Catholic hierarchy over the Commission's investigations.
The Commission, chaired by Judge Yvonne Murphy and set up in March 2006, is examining a representative sample of 46 priests and is due to finish in September 2008.
However, two senior prelates who asked not to be named told the Sunday Independent that there was anxiety within the hierarchy over the length of time it could take to complete its work.
The progress of the inquiry was discussed at the last Bishop's conference in December, according to clerical sources, and general concerns were expressed by bishops.
"There is this anxiety about it. This inquiry, if you like, is quite new. It's a whole new thing and it is like the tribunals, it develops its own life and nobody knows really where it is going to end," said one bishop who asked not to be named. "There would be concern and obvious anxiety about the whole thing."
Cardinal Connell's legal challenge took the Catholic hierarchy by surprise. Archbishop Diarmuid Martin learned of the challenge on the eve of the High Court action last Thursday.
The court heard that the Cardinal was before the Commission -- which meets in private -- on October 5 when his legal team discovered that the Commission had a document which was covered by legal privilege.
Cardinal Connell hadn't waived his legal privilege over the document and wanted to know how the Commission got hold of it. It emerged that Archbishop Martin had agreed to release the documents to the Commission in June last year. He had agreed to waive legal privilege, something which the Cardinal's lawyers argued he was not entitled to do.
Victims' groups have pleaded with Cardinal Connell to co-operate with the inquiry. Colm O'Gorman, the former director of One in Four, said a precedent was set when confidential Church files, including legal advice, were released to the Ferns Inquiry into clerical sex abuse.
He said Cardinal Connell's action could scupper the inquiry. "If this action is successful and if the inquiry is unable to examine the documents relating to the way the Diocese handled the priests who were accused of sexual abuse, then clearly it cannot do its job effectively."
The Bishop of Killaloe, Willie Walsh, said while he couldn't comment on the court proceedings, there was a need for sensitivity. "The whole thing of child abuse has been an enormous tragedy and I think all of us have to be as sensitive as absolutely possible to the victims of abuse," he said.
"We also have to be careful that natural justice is observed as well at all times. It is a very difficult situation."
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