Cardinal George Pell had an “unusual” and close early involvement in handling the complaint by a former altar boy which eventually led to a court decision insulating the Catholic church in Australia against liability in cases of sexual abuse by priests, the child sex abuse Royal Commission has heard.

John Ellis was 13 years old in 1974 when Father Aidan Duggan of Bass Hill parish seduced him into a sexual relationship which continued for 13 years. By the time Mr Ellis recognised the relationship was abusive it was the mid 1990s and he was a husband and father.

As Archbishop of Sydney, Cardinal Pell was informed of Ellis’s complaint within a month of it being made in 2002. Documents tendered to the Commission reveal that from then on the Cardinal actively participated in a bumbling and insensitive process which defied the church’s own “Towards Healing” protocol. The result was an “absence of justice” for Mr Ellis according to an internal Archdiocesan review.

Cardinal Pell was then and still is a member of the Australian Catholic Bishop’s Conference which set up the Towards Healing protocol with the warning that “if we do not follow the process and procedures of this document we will have failed our own criteria.”

Towards Healing required an assessor to be appointed to establish whether or not a  complaint was likely to be true before a facilitation meeting was held to discuss issues of redress. In Mr Ellis’s case, no assessment was carried out before Cardinal Pell wrote to him in December 2002 saying “a clear resolution of this matter is not possible” and “under the circumstances I do not see that there is anything the Archdiocese can do”.

The basis of this letter, the Commission heard, was the view of John Davoren, then director of the Church’s Professional Standards Office, conveyed in a letter to Cardinal Pell two weeks earlier. Mr Davoren argued the facts could not be established because “it does not appear that Mr Ellis can corroborate his version of events in such a way that it would be possible to conclude on the balance of probabilities that the situation that he described did in fact take place.”

In his evidence to the Commission, Mr Davoren said he reached this conclusion because there had been no other complaints against Duggan, because there was “nothing Mr Ellis was able to indicate to point in that direction” and because he thought Mr Ellis “may have had a memory problem”.

He agreed that he had not asked Mr Ellis for any corroborating documents. The priest who abused Mr Ellis had not been interviewed about the case because he was old and deemed unfit to provide meaningful responses.

“Your view is you could never be satisfied if you just had the account of one person and nothing else?” counsel assisting the commission Gail Furness SC asked.

“That is where I was coming from, yeah”, Mr Davoren replied.

Cardinal Pell wanted a briefing before he made a decision about facilitation in Mr Ellis’ case, correspondence tendered in evidence showed. This was “unusual”, Mr Davoren said. He admitted the proposed facilitation fell outside the Towards Healing protocol, being “simply a way of making sure that Mr Ellis was not just left without any contact at all”.

In December Cardinal Pell wrote to Mr Ellis in harsher terms than Mr Davoren had proposed. His letter omitted an assurance that the church’s stance didn’t mean Mr Ellis was disbelieved, and omitted an expression of regret for any hurt Mr Ellis had incurred. The assessor eventually appointed to Mr Ellis’ case concluded on the balance of probabilities that the abuse had occurred. Even so, the church disputed whether it occurred in the litigation and its solicitors vigorously challenged Mr Ellis’ character and credibility over days of cross-examination.

The litigation and later ex gratia payments to Mr Ellis cost $1.5 million. Mr Ellis said he got the impression from a meeting with Cardinal Pell in 2009, after the protracted and personally devastating litigation which he lost, that the Cardinal had been  “completely out of the loop” in the decision making on his case. He said the Cardinal told him that if he had known of Mr Ellis’ offer of compromise before the proceedings commenced, “there is no way I would have spent more on legal costs than you were asking for”.

Correspondence tendered to the Royal Commission shows Cardinal Pell instructed his solicitors Corrs Chambers Westgarth through his private secretary Dr Michael Casey to decline Mr Ellis’ offer to settle for $750,000 plus costs in 2004.

Mr Ellis gave evidence that he was told someone in the church had taken a set against him, but he didn’t believe it was Cardinal Pell.

Cardinal Pell is expected to give evidence next week.

The hearing continues.