The government has fundamentally misunderstood deradicalisation and is taking an approach that has no previous evidence of success, according to a key adviser on intervention programs.

Clarke Jones, founder of the Australian Intervention Support Hub, has made stinging assessment of the approach to dealing with young extremists like the 16-year-old boy arrested on Sunday over an alleged Anzac Day plot.

Messages from the Auburn teenager were intercepted over the weekend as he chatted online to a male overseas, allegedly saying he was trying to source a gun to use for an Anzac Day massacre.

The boy had reportedly been placed into a government-run deradicalisation program a year ago after Islamic State recruiter Neil Prakash tried to involve him in another plot.

"The government is certainly on the wrong track," said Dr Jones, whose Support Hub within the Australian National University is partly funded by federal grants and informs government policy.

"The fundamental principles of community relations and strong community partnerships is flawed because, at the moment, those relations have not been built and, in many cases, they have been broken for various reasons. Without community engagement, we're right up against it."

The boy's family gave an anonymous interview to The Australian last year for a story lauding the federally funded National Disruption Group, a new $32.7 million multi-agency approach led by the Australian Federal Police.

Potential extremists are referred to the group and a suite of agencies come up with a tailored program to deradicalise individuals.

In the case of the 16-year-old boy, who was reportedly skipping school and chatting online to extremists, he was given a gym membership, started an electrician apprenticeship, started attending English-language sermons at a mosque with his father and had regular visits from police community contact workers, the family said.

They believed he was improving however police stormed their Auburn home for the second time on Sunday and charged him with doing an act in preparation or planning for a terrorist act

The boy's lawyer, Zemarai Khatiz​, entered a not guilty plea in Parramatta Children's Court on Tuesday and indicated he would make a bail application on Friday.

He said a psychologist will assess the boy in prison and evidence of the impact of long-term incarceration while awaiting trial will be a "very relevant and powerful factor" in the application.

Experts within the deradicalisation sphere have acknowledged that there is no clear evidence about what works and what doesn't work.

An audit of 87 federally funded "countering violent extremism" programs between 2010 and 2014, published in the Behavioral Sciences of Terrorism and Political Aggression journal, found just one targeted radicalised individuals and most programs were self-evaluated only.

Dr Jones said the government needed to "let go" of some control and allow programs to be more community-led. He said police were "overwhelmed and often wrongly placed to be at the heart of these programs".

"Because of the lack of any connection to community or social issues, these programs lack all of the nuances required to address the problem," he said. "The government needs to stop what they're doing, examine, reassess and scrap things that aren't working."

A spokeswoman for Justice Minister Michael Keenan said no program can ever guarantee a 100 per cent success rate.

"We have implemented robust programs, based on best available research and international best practice," she said. "The professional and community sectors are crucial partners in delivering these services."