The treatment of children in Western Australia's justice system is a colonial system akin to religious institutions in terms of their secrecy and mistreatment of children, an inquiry into youth justice has heard.

Appearing at the Senate hearing into Australia's youth justice and incarceration system, George Newhouse, the chief executive for the National Justice Project, said it was his observation there was no therapeutic support for children in custody.

"Children in detention are treated as outcasts in society...just as children in religious orders were treated in the past," Professor Newhouse told the inquiry.

"Very few of the people who go into these institutions [as observers] are able to reveal what is going on."

He argued police and police unions actively contribute to this by protecting their members over the rights of children.

"We are talking about colonial institutions; they instill fear in themselves," Professor Newhouse said.

The inquiry has come about after the death of two children in custody in WA in the last 18 months.

The inquest into the death of 16-year-old Cleveland Dodd, who took his own life in Unit 18 - a small area for youth detainees in the maximum-security Casuarina Prison in Perth's south - has revealed a litany of lies and mistruths amongst government departments.

Nonetheless, the WA government has remained unmoved on their housing of children in Unit 18 and have routinely commented on the behaviour of the children in custody, rather than addressing the myriad of complicated issues at play.

"Children with suicidal ideation end up in solitary confinement…behavioural issues are punished…there's no therapeutic care in youth detention," Professor Newhouse said.

Last week, it was revealed 27 First Nations children and young people self-harmed and/or attempted suicide whilst in custody in the last financial year, with another 135 children receiving psychological or medical treatment without hospitalisation.

Highlighting data from WA which found 36 per cent of children sentenced to youth detention had Fetal alcohol spectrum disorder (FASD), Professor Newhouse added: "When they get into youth detention, they get no support; no one cares."

"If they complain, no one is listening…it is abusive."

Dr James Beaufils from the Jumbunna Institute said the overrepresentation of children isn't "something new".

He said children on remand was an "underutilised" area of research, especially regarding the lack of treatment they receive in custody.

Furthermore, he added it should only be used in the most "extreme circumstances".

"But it's not," Dr Beaufils said.

Their treatment of children in detention was heavily criticised by Professor Newhouse, who said he has acted on behalf of children who had been housed in solitary confinement for more than 300 days.

"They [the WA government] don't want the public to know what happens to these children," he said.

"They will lose in the end, but they will fight to hide the horrors of what goes on in these institutions."

The latest productivity commission report revealed it costs over $3,000 per child, per day to house young people in youth detention, or more than a million dollars per year, prompting him to exclaim: "You could put them up in the Hilton…surely, we can do better than that?

"They [the WA government] don't want to spend the money on alternative solutions and support to divert them away from the prison system," Professor Newhouse said.

"They [young children] need healthcare and education, not punishment…they're not listening.

"It's a protection racket."