The NSW Special Commission of Inquiry did not consider allegations last year about police involvement in the church’s Professional Standards Resource Group (PSRG) between 1998 and 2005.

This was despite a submission by Hunter detective Peter Fox to expand the inquiry to investigate the PSRG, and the production of police documents to the inquiry in June last year by NSW Greens justice spokesman David Shoebridge.

‘‘These are matters of the utmost seriousness with profound implications for public confidence in the administration of justice in NSW,’’ Mr Fox told the NSW Special Commission of Inquiry in a six-page submission on June 22, 2013.

Police acceptance of confidential arrangements with the church was ‘‘preposterous and contrary to its statutory duties and obligations’’, Mr Fox wrote in his submission.

Police documents obtained by Mr Shoebridge were central to a Police Integrity Commission (PIC) inquiry in October which was told NSW police officers may have ‘‘condoned’’ and even ‘‘encouraged’’ the cover-up of child sexual abuse by the Catholic Church.

In a speech to Parliament after the PIC inquiry, Mr Shoebridge said it was ‘‘absolutely remarkable’’ that the NSW Special Commission of Inquiry, headed by Margaret Cunneen, SC, did not look at the matter, given her inquiry was launched after Mr Fox’s allegations of improper relationships between police and the church on  Lateline in November 2012.

‘‘The Cunneen inquiry rejected the key evidence about the culpable arrangements between the police and the church. In rejecting that, it rejected Detective Chief Inspector Fox’s conclusions. The report is fundamentally flawed,’’ he said.

The Cunneen inquiry advised Mr Shoebridge on June 25, 2013, that the ‘‘submissions had been forwarded through the appropriate channels for consideration’’, but did not explore the matters raised.

It ‘‘understood’’ the Professional Standards Resource Group was ‘‘not involved in the exchange of information between the Catholic Church and police’’.

Ms Cunneen was advised there was no evidence the resource group ‘‘dealt with any matter’’ involving Hunter paedophile priests Denis McAlinden and Jim Fletcher, who were the subject of the Cunneen inquiry.

The advice was contradicted in October this year when the Police Integrity Commission was told McAlinden was the subject of a ‘‘blind report’’, where the church and police shared details of child sex allegations without naming the offender.

In his speech to Parliament, Mr Shoebridge described the Police Integrity Commission hearing as a ‘‘long overdue opportunity to take an independent look at the arrangements that led to a NSW police officer, a sworn officer, being involved on an internal and highly controversial Catholic Church body’’.

The arrangement allowed the church to believe it had satisfied its obligations to report child sex crimes, he said.