It took nearly 20 years for the Vatican to dismiss a Wollongong parish priest after allegations against him first emerged, the royal commission into child sexual abuse has heard.

Father John Nestor was charged and convicted of indecently assaulting a 15-year-old altar boy in Wollongong in 1996. A year later he was acquitted on appeal.

When further allegations surfaced about him engaging in inappropriate behaviour with boys at holiday camps, the local diocese tried to have him removed from the ministry.

Counsel assisting the commission Angus Stewart told the hearing the Vatican upheld an appeal by Mr Nestor in 2001.

"The congregation ruled that the Towards Healing Assessment process had not complied with the procedural requirements for an preliminary investigation under canon law," he said.

It took another seven years before Mr Nestor was dismissed by Pope Benedict in 2008.

Mr Stewart told the hearing that documents had been sought from the Vatican in relation to Mr Nestor.

"It's expected that the evidence will reveal that the period traversed by the facts of this case study, 1996 - 2009, there was confusion both in the Holy See and the wider Catholic Church where in the Curia of the Holy See jurisdiction over allegations of child sexual abuse by clergy lay," Mr Stewart said.

The general secretary of the Catholic Bishops Conference, Father Brian Lucas, has given evidence at today's hearing.

He interviewed Mr Nestor at the Bishop's request but says the then-Father denied any wrongdoing or inappropriate conduct.

"As it was presented to me there was some allegation and denial and my task was to see if I could work through that impasse," Father Lucas said.

Under questioning by Commissioner Peter McClellan, Father Lucas told the hearing that no record of the conversation was kept because it was confidential.

He said he felt confidential conversations were better to elicit an admission or freer response by a priest who had come under questioning.

The commission is examining the Vatican's actions in dealing with the allegations against Mr Nestor.

Francis Sullivan from the Truth Justice and Healing Council says it is the first time a public hearing into child sexual abuse has examined the role of the papacy.

"The head of the Royal Commission, Justice McClellan, has already stated publicly that it has sought documents from the Vatican and in this particular case received documents around this whole process," she said.

The hearing continues.