The Darwin boy was due to appear in a children's court on Thursday following a joint investigation by Australian Federal Police, Northern Territory Police and the Australian Security Intelligence Organisation.
The NT Joint Counter Terrorism Team began an investigation earlier in October after receiving information via Crime Stoppers about violent extremist material suspected to have been posted online by an Australian user.
Inquiries revealed the teen operated social media channels where it's alleged he accessed, discussed and reposted extremist material.
Investigators executed search warrants in Darwin on Wednesday, seizing documents and electronic devices which allegedly contained the extremist material and referenced violent attacks. Â
They also identified alleged instructions for making 3D-printed firearms and other documents and manuals investigators allege were likely to facilitate a terrorist act.
The teen was charged with collecting or making documents likely to facilitate terrorist acts, carrying a maximum penalty of 10 years in prison.
He was further charged with possessing violent extremist material obtained using a carriage service, carrying a maximum penalty of five years' imprisonment.
A third charge against the teen was that of possessing or controlling firearms and explosives manufacture material obtained or accessed using a carriage service, carrying a maximum five years in prison.
AFP Counter Terrorism Commander Paula Hudson said on Thursday investigators were becoming increasingly concerned about the number of young people coming to their attention.
''It is well-documented that terrorists and violent extremists use the online environment to radicalise vulnerable individuals, and technology is enabling this to occur a rapidly increasing rate," she said in a statement.
''The speed and scale of radicalisation is becoming one of our most significant challenges, especially when it comes to young people."
A whole-of-society effort was needed to protect young people from radicalisation and manipulation, Commander Hudson said.
''Without a serious intervention, the risk is our justice systems, mental health systems, education systems and financial systems will become overwhelmed by youth victims and perpetrators."
NT Police Acting Commander Mark Grieve said it was deeply concerning to see allegations of this nature involving a young person, particularly where violent extremist material and information about the manufacture of firearms is alleged to be involved.
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