A former journalist accused of threatening to behead members of a Canberra church will fight charges linked to messages he allegedly posted on social media.

Key points: James Waugh's lawyer submits a plea of not guilty on his behalf

James Waugh's lawyer submits a plea of not guilty on his behalf The former Queanbeyan Age journalist is accused of threatening to behead Christians

The former Queanbeyan Age journalist is accused of threatening to behead Christians The threats were allegedly made on social media

James Michael Waugh, 28, was arrested at his Griffith home in April after allegedly making the threats, including a Facebook post in which he said he was "going to kill" members of a Canberra church group.

The former Queanbeyan Age reporter was charged in the ACT Magistrates Court with threatening to act with intent to cause public alarm, using a carriage service to menace others and possessing a weapon to be used to kill.

He has been in custody since.

Mr Waugh was not present in court when his lawyer entered pleas of not guilty to the charges on Wednesday morning.

The prosecution told the court that Mr Waugh could be charged with further offences in the future.

Court documents said police raided Mr Waugh's home after a tipoff to the National Security Hotline.

The threats allegedly included a Facebook post on the Canberra House of Prayer page, which read "I'm going to kill every single one of you dog polytheist c***s."

A post allegedly from James Waugh on the Facebook page of a local Canberra church group. ( Facebook )

Mr Waugh also sent messages to a Facebook Messenger group chat.

"I have issued threats, along with my name and address, to every coward dog church in Canberra," he allegedly wrote.

"If you know someone with balls send them along. I've bought a scimitar [Middle-Eastern curved sword] and intend to cut their heads off in my front yard as a reprisal."

According to court documents, Mr Waugh told police the threats on social media were aimed at Trinitarians, and that he had issued the threats to any local Christian church he was able to locate.

Mr Waugh also allegedly told police he had purchased the one-metre-long scimitar in Pakistan.

The court has previously heard that a mental health assessment found Mr Waugh had no mental illness to explain his behaviour, with a prosecutor saying he had displayed "extreme religious beliefs".

On Wednesday, Special Magistrate Margaret Hunter ordered the accused to appear in person the next time his matter was in court, which is scheduled to be a pre-trial hearing in July.