WARNING: This story contains graphic content that may upset some readers

A former army apprentice fought back tears as he told a royal commission about the horrific abuse he allegedly suffered at a military training school, including beatings and a sexual assault involving a dog.

The former serviceman, given the pseudonym CJU, is one of five witnesses to give testimony about alleged abuse at the Army Apprentices School in Balcombe, Victoria in the 1960s and '70s.

The witness, who enlisted in 1978 as a 15-year-old apprentice, told the Royal Commission into Institutional Responses to Child Sexual Abuse he was physically and sexually abused by senior apprentices and staff.

In testimony, he recalled one night when older recruits stripped him and smeared Vegemite on his groin and genitals before bringing in a dog to lick it off.

"I was scared the dog was going to bite my genitals," he said.

He told the commission the older boys then attempted to force the animal against his backside .

"They said, 'This is the only way you're ever going to have sex. You're a dog for reporting us. If you tell anyone about anything else, the next time it will be worse and we'll kill you'."

The commission heard CJU believed the alleged attack was in retribution for a report he made to staff about a physical assault that left him with a broken arm.

He gave testimony that senior staff at the school fobbed off complaints of abuse.

"We were told by the staff that these things happened all the time and that we needed to get on with daily life," he said.

The witness, who left the army in 1989, told the commission the Australian Defence Force silenced abuse.

"The military were my guardians and they covered this up," he said. "What happened to me never should have happened."

CJU received a round of applause from the hearing room as he left the stand.

A former commanding officer of the Army Apprentices School in Balcombe told the inquiry he was unaware of abuse at the facility.

Alan McDonald, who served at the centre from 1972 to 1976, told the commission he was stunned to hear the witnesses' stories.

"I was shocked," he said. "I didn't know that had occurred. I was really saddened to hear the stories that we heard. I'm sure all the people here are shocked at what they heard."

When asked by commission chairman Justice Peter McClellan​ whether, as commanding officer, he should have known, Mr McDonald replied: "Everyone's got an opinion on that."

Mr McDonald told the inquiry that reticence from the alleged victims was a reason he was unaware of the abuse.

"They never reported any of these things," he said. "They kept it to themselves."

The Department of Veterans' Affairs was ill-equipped to handle sexual abuse complaints, the inquiry heard.

Adair Donaldson, a lawyer acting for about 50 people who suffered sexual abuse as minors at the ADF, told the commission that lodging a claim with the DVA could be traumatic and forced claimants to "jump through hurdles" dbecause of its high threshhold of proof.

"It is not set up to handle broken minds as a result of surviving sexual abuse," he said.

DVA compensation and rehabilitation manager Neil Bayles told the inquiry the department did attempt to find evidence to support a victim's claim but "in these cases, evidence is very difficult to get".

The hearing is scheduled to run until July 1.

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