The Salvation Army told two women raped as children by their Sunday school teacher not to go to police or the media, an inquiry has heard.

In a second hearing about the Salvation Army, the royal commission into child sexual abuse is examining how the charitable organisation responded to complaints from abuse victims in the 1990s and up to the present day.

Simeon Beckett, counsel advising the commission, said evidence would show the two women raped as children by Salvation Army Envoy John Lane, when he ran a Sunday school at Fortitude Valley, Queensland between from 1971 to 1984, were initially not believed when they reported the abuse.

One of the victims, JG, was 10 years of age when she was raped.

She and another victim of Lane's, JD, reported the rapes and frequent sexual assaults in early 1992 to Colonel Stan Everitt, the army's divisional commander for southeast Queensland.

Mr Beckett said the commission would hear Mr Everitt's response to JG and JD was "are you sure you are not lying, are you telling me the truth? People make up these types of allegations."

Mr Everitt told both girls Lane was a Korean War veteran and a good man.

He "instructed both JG and JD not to go to the police or the media with that information," Mr Beckett said.

However, in June 1992, Mr Everitt terminated John Lane's services at Prince Charles Hospital because of allegations of sexual misconduct, Mr Beckett said.

In April 1997 JG and JD went to police and Lane was charged with five counts of sexual assault and sentenced to 16 months in prison.

Lane has since died.

Mr Beckett said the Salvation Army had visited Lane in prison to offer him support.

He also said the commission would hear JG's early rejection by the Salvation Army made her feel she was "abused all over again and the impact was severe for her".

JG was later offered an apology and $80,000 by the Salvation Army in compensation, for which she was required to sign a deed of release.

In August 2007, Major Peter Farthing who heads the Army's Personal Injuries Complaints Committee (PICC) wrote to JD and said that in 1992 "some older people were still unaware of the reality of sexual abuse" and the damage it caused.

"I suspect that if Lieutenant Colonel Everitt failed in any of these ways, then he was a representative of his generation. This kind of failure was sadly not uncommon in Australian society and even in Christian churches," Mr Farthing wrote.

The hearing in Sydney continues.