And the Salvation Army's leadership often failed to discipline or remove the perpetrators, but simply moved them to other homes where they frequently continued the abuse.

The revelations came during the first public hearing in Sydney by the Royal Commission into Institutional Responses to Child Sexual Abuse for 2014.

In his opening address, counsel assisting the commission, Simeon Beckett, said the focus of the hearings would be on the "contemporaneous response by the Salvation Army and relevant government agencies to child-sex abuse within the Alkira home for boys in Indooroopilly, Queensland; the Riverview Training Farm, also in Queensland; Bexley Boys' Home in North Bexley; and the Gill Memorial Home in Goulburn".

"It will examine processes at the time to identify, investigate, discipline, remove, dismiss and/or transfer persons accused of or found to have engaged in child sexual abuse," he said.

"The evidence will explore whether those who maintained the homes jointly engaged in child sexual abuse and whether the position of manager was used to frustrate the making of complaints of sexual abuse and their investigation."

The commission will focus on the alleged abuse inflicted by Salvation Army officers Lawrence Wilson, Russell Walker, Victor Bennett, John McIver and Donald Schultz on boys aged from about six to about 17.

On Tuesday, it heard that the violence and sexual abuse inflicted on the boys at the homes was at "the severe end of that examined by the commission" during the course of its investigations.

"The boys were frequently punched with a closed fist, thrown on the ground with force, hit with straps until they developed welts or bled," Mr Beckett said.

They were repeatedly anally raped and forced to undertake oral sex on their house parents. They were also abused by other boys at the homes.

One witness, ES, is expected to tell the commission that he was placed in a cage on the verandah of the Riverview home for nine days.

Upon his release, he was allegedly sodomised by Mr Bennett, his house parent.

Mr McIver allegedly broke one boy's arm during an assault and on another occasion refused to allow a boy with a dislocated shoulder to attend hospital, instead forcing the injured shoulder "back into its socket".

Boys who complained were often disbelieved and severely punished, Mr Beckett said.

"Some will indicate that even when they ran away they were returned to the home where they were physically punished," Mr Beckett said.

"Many didn't complain due to fear of punishment and retribution."

At the Riverview farm, one witness would tell how he was made to sort fruit and vegetables given to the farm to feed the animals, picking out what could be given to the boys, Mr Beckett said. If he made a wrong choice, he was flogged.

"Other forms of punishment included sweeping the playground with a toothbrush, cleaning 50 pairs of shoes ... and on one occasion forcing a boy to eat his own vomit."

Mr Beckett said the Salvation Army had a policy of simply moving officers to different homes rather than properly disciplining them or ensuring they had no further contact with children.

He said the commission would hear from two former house parents, Cliff and Marina Randall, who were dismissed after making a complaint against Mr McIver.

Three of the five officers being examined are still alive - Mr McIver, Mr Schultz and Mr Walker.

Only one was charged; Mr Walker with an act of indecency.

They deny the allegations against them.

Mr Wilson died in 2006.

The hearing continues.