Teenage Australian Defence Force recruits were subjected to horrific sex acts and a pattern of intimidation that allegedly caused one to suicide, a royal commission has been told.

In his opening address to the Royal Commission into Institutional Responses to Child Sexual Abuse, counsel assisting the commission Angus Stewart, SC, said navy recruits were subjected to "ritualised practices of bastardisation that were designed to break in and humiliate new entrants".

The practices included "blackballing" or "nuggetting", where recruits would be held down while boot polish was smeared on their genitals or anal area with a hard brush; a "royal flush", where recruits would have their heads flushed in a toilet after it had been used; and "gotcha", where they would have their genitals pinched in the showers.

The inquiry, being held in Sydney this week, will examine the conduct of the ADF Cadets division from 2000, and the ADF's treatment of apprentices at ADF facilities from the 1960s onwards.

On Tuesday, the royal commission heard the ADF had threatened to dishonourably discharge 15-year-old cadet Eleanore Tibble on "fraternisation charges", after an instructor 15 years her senior had a sexual relationship with her.

Mr Stewart told the commission that Eleanore was upset about the possibility of being discharged and suicided in 2000. The ADF had not told her it was no longer pursuing charges.

Eleanore's mother, Susan Campbell, is one of more than 110 people who have contacted the commission for its inquiry into the Australian Defence Force.

Glen Greaves, who joined the navy in 1971 and appeared before the commission wearing his service medals, gave evidence that as part of a pattern of abuse he was dragged out of bed, had paper stuffed in his mouth and a broomstick repeatedly shoved into his anus.

"I wore my medals for a reason," an emotional Mr Greaves told the commission. "I wanted to serve my country and I regret that some of my childhood years weren't the way I had planned."

The commission also heard evidence from a man given the pseudonym CJA, who joined the navy at Leeuwin in Western Australia in 1967.

"On multiple occasions I was snatched in the middle of the night and dragged to a sports oval," he said.

"I was forced to suck another recruit's penis or lick a junior recruit's anus. This was often after another recruit had been buggered by an older recruit and ejaculated into.

"Other times I was forced to have anal intercourse with junior recruits or I was raped by another junior recruit who was directed to do so by the older recruits or base staff," said CJA. "This happened repeatedly."

CJA said the advice he received from his seniors was: "Suck it up boy, I did it, and it will make a man of you."

He told the commission he learnt quickly what happened to those who complained.

"I watched a cook masturbate and ejaculate into an officer's mashed potatoes, before returning it to the officer."

Another witness, CJT, described how the senior recruits at Leeuwin dragged him out of the shower and held him down by the shoulders.

"[One of them] then exposed his penis to me and said: 'Don't think you can get away that easily. Now you'll suck this.'

"Then they rolled me over and applied shoe polish to my penis and scrotum and started scrubbing it with a brush.

"I was left lying on the tiles, bleeding, with black shoe polish all over my penis and scrotum."

Former navy recruit Graeme Frazer said he was also subjected to the practice described by CJT, known as "nuggetting."

He told the commission he was forced to run down a corridor called the "gauntlet" while being hit with sacks filled with irons, boots and other items.

In 2001, Mr Frazer had his compensation claim to the Military Compensation and Rehabilitation service rejected on the basis that he did not have enough corroborating evidence.

Three years later, the Administrative Appeals Tribunal overturned the decision.

The judgement acknowledged there was a culture of "bullying, harassment, intimidation, bastardisation, victimisation and violence" at Leeuwin and "that such activities was either effectively condoned by the officers in control of the facility, or that no effective steps were taken to wipe out or minimise these practices".

The commission also heard on Tuesday that some survivors feel their voices are not being heard.

The opening address was interrupted by alleged sexual abuse survivor Robert McJanett, who claimed that by restricting the scope of the inquiry into cadets from the year 2000 onwards, the inquiry had omitted hundreds of victims' voices.

"We are just rubbish for you to flush down the toilet, this is the biggest cover-up in the country," the 55-year-old said, before being removed from the hearing.

Mr McJanett told reporters that from the age of 12 he was allegedly repeatedly raped and molested by an Air Force Officer at a Queensland high school cadet program in the 1970s.

He urged the royal commission to widen its inquiry into the state government-run cadet programs that existed prior to 2000.

The commission heard the Defence Force has already taken some steps to address systemic issues identified by two previous inquiries, the Abuse Response Taskforce and the Piper Review.

The Vice-Chief of the Australian Defence Force, Vice-Admiral Ray Griggs, has been called to give evidence of institutional responses to the commission.

The hearing continues.