Ireland's ongoing paedophile priest scandals have taken a bizarre turn with two of the country's top Catholic clerics clashing in the courts over secret church files.

Cardinal Desmond Connell and Archbishop Diarmuid Martin are battling over the proposed publication of files relating to the former's handling of complaints against paedophile priests.

The unprecedented move to hold up publication has prompted claims of a church cover up by a senior Irish canon law expert.

Connell, 81, went to the high court this week to prevent an Irish state inquiry from examining files concerned with clerical child abuse while he was in charge of the church in Dublin.

Connell was urged to resign when a major abuse scandal was exposed in the Irish capital six years ago. He was accused of ignoring victims' allegations of abuse and failing to act against priests accused of paedophile activities.

Martin, a former Vatican diplomat and rising star of the Irish Catholic church, wanted to hand over the files as part of his policy to create more openness in the Dublin diocese.

But without informing Martin, Connell went to the high court on Wednesday night to seek an injunction preventing the files from being handed over.

The documents are understood to relate to legal advice Connell and other members of the Catholic hierarchy received following claims of widespread child sexual abuse in the Dublin diocese.

Although Connell previously promised the Irish police and victims' groups that a new independent inquiry would have full access to church files, he argued that the documents were privileged and protected by lawyer-client confidentiality.

Leading Irish canon lawyer and priest Tom Doyle has openly accused Connell of a cover up.

"The only reason why Cardinal Connell would seek to prevent access to the files is because they contain incriminating evidence. He is attempting to hide behind legal doctrine. This is not privileged information,' he said.

A spokesman for Connell said he was in a hospital in Rome after falling during a visit to the Vatican and was not available to comment.

At present there are 450 legal cases taken by victims of clerical abuse in Dublin alone.

Martin's own inquiry team has also identified 147 priests and members of religious orders against whom allegations of sexual abuse were made over the last 60 years.