A New South Wales inquiry into child sexual abuse in the Hunter Valley's Catholic Church has heard that a boy was told to repent his sins after telling his priest he had been abused by clergy.

Part two of the inquiry got underway this morning and is investigating claims by senior policeman Peter Fox that the church did not cooperate with police over abuse allegations against two priests - Father James Fletcher and Father Dennis McAlinden - and instead tried to protect them.

In her opening remarks, counsel assisting the commission Julia Lonergan said the inquiry will hear evidence that a boy abused by McAlinden between the ages of five and nine told his Singleton parish priest about it during his first confession.

"This boy was given penance apparently for his sin in being abused by that priest," she said.

Ms Lonergan also told the court that evidence will show McAlinden was sent overseas in 1993, just months after the then bishop moved to defrock him because of serious abuse allegations.

"We anticipate evidence will suggest that a plan was made for McAlinden to be sent overseas to England at or around that time," she said.

She also said there are church documents from a meeting in May 1976 that show senior clergy agreed McAlinden should leave the New South Wales parish of Foster because of abuse allegations.

The next day, McAlinden quit, headed for Geraldton in Western Australia.

Ms Lonergan told the court three police investigations involved McAlinden.

"We expect that the evidence gathered by this inquiry will show that the Maitland Newcastle Diocese, as an institution, had extensive knowledge dating back to the 1950s of the serious risk posed to children by McAlinden," she said.

In opening the inquiry this morning, Commissioner Margaret Cunneen SC told the court abuse by a priest was a gross breach of trust.

"The sexual abuse of children is abhorrent," she said.

"It has a devastating and long-lasting effect on victims and their families."

Commissioner Cunneen told the court that in 2010, the former bishop of Maitland-Newcastle, Michael Malone, described McAlinden as a predator who could have been dealt with earlier.

"McAlinden and Fletcher were sexual predators who, utilising their positions as priests of the diocese, separately committed heinous offences against vulnerable young children," she said.

The commissioner acknowledged those from the Hunter region who were clergy abuse victims, saying the diocese had a troubled history.

The first half of the inquiry, which wrapped up last week, examined claims that senior police told Detective Chief Inspector Fox to stop investigating the two paedophile priests.

The second stage of the inquiry is expected to last three weeks.

The commissioner is expected to have her report finalised by September and says she wants it made public as soon as possible.