Former Moree Catholic priest Father John Joseph Farrell "only fondled genitals as it was his way of showing affection" a church official allegedly told the parent of an abused altar boy, a royal commission has heard.

The Royal Commission into Institutional Responses to Child Sexual Abuse is looking into the behaviour of Father Farrell, who sexual abused altar boys in Moree in the 1980s, and how the Catholic dioceses of Armidale and Parramatta handled complaints about him.

Karolyn Graham told the inquiry that in 1984 her former husband, Patrick, went to see the Vicar-General of the Armidale Diocese, Monsignor Frank Ryan, after their nine-year-old son Michael McGroder revealed he had been touched inappropriately by Father Farrell.

"Monsignor Ryan asked [my husband] not to go to police as it would be traumatic for Michael and the family and asked whether we wanted to see our boy in a witness stand being torn to pieces," Ms Graham told the royal commission.

"Patrick also said that Monsignor Ryan told him that Father Farrell said to him that 'he loved the boys, he didn't mean to do them any harm, he only fondled their genitals as it was his way of showing affection'.

"I remember when Patrick came home and told me [this] I was horrified and felt intimidated by the church."

Michael McGroder, now 43, told the inquiry that Father Farrell touched him inappropriately on a road trip in the summer of 1984.

He said Father Farrell was driving him from Moree to a mass on a country property in Goondiwindi when he repeatedly touched him on his knee, leg and crotch.

Despite rejecting Father Farrell's advances, Mr McGroder said the priest would not stop.

"He said 'you know I was only playing don't you?'," Mr McGroder told the commission.

"I said 'no, I don't like it' and he said 'I'm only having fun, I do it to all the boys'."

Mr McGroder said when he later asked other altar boys whether they had been touched by Father Farrell they said their abuse was worse.

He told his mother and father a couple of weeks later, who then tried to rally other parents to complain.

Mr McGroder and Ms Graham told the royal commission their family was ostracised by the Moree community and they lost many friends because of their efforts to raise the alarm about Father Farrell.

"Father [Richard] Gleeson told Dad that he had driven [a] wedge through the community and had divided it," Mr McGroder said.

Father Farrell claimed to be a 'new man', commission hears

Counsel assisting the royal commission Gail Furness SC told the inquiry Father Farrell was sent to one counselling session with a psychologist in May 1984 and told Bishop Henry Kennedy he was a "new man" upon completing it.

In 1984 he was moved out of Moree and spent time in Tamworth, Sydney and Parramatta in the years that followed.

Mr McGroder and his family eventually moved to Sydney and cut ties with the Catholic Church.

He said he would like an apology from the church, but feels it would be insincere.

"The individual will be punished but the church will not be — the arrogance is beyond belief," Mr McGroder said.

"They have not said sorry to me, not said anything to my family, so many people's lives have been ruined because of the attitude of the church."

The royal commission will hear from three priests from the Diocese of Armidale, the former Bishop of Armidale and the former Bishop of Parramatta, who will each be questioned about what they knew of Father Farrell's behaviour and what they did about it.

The hearing is set down for two weeks.