NSW man Cameron Robert McKay is accused of an assault on a 67-year-old woman in February that left her needing surgery.

McKay, in his mid-30s, was set to front the ACT Magistrates Court on Thursday but failed to appear.

Chief Magistrate Lorraine Walker said McKay had written to the prosecution and the court, asking to "appear by way of special appearance".

Ms Walker said the affidavit he provided in support of his application was "gobbledygook".

"It does not address the matter before the court," she said.

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McKay is charged with recklessly inflicting grievous bodily harm, trespassing on premises and failing to comply with a magistrate's order.

A prosecutor had asked Ms Walker to issue the warrant, saying McKay described himself as a sovereign citizen and did not believe in the court's jurisdiction.

The lawyer said this was the fifth time the matter had come before the court and another magistrate on the previous occasion said a warrant was likely to be issued if he failed to appear.

McKay was charged in May after NSW Police helped execute a search warrant at an address in Sydney's west, where he was arrested.

He initially appeared at the Blacktown Local Court where he was granted bail to appear in the ACT Magistrates Court.

Detective acting inspector Leesa Alexander at the time said Canberra had seen some of the ongoing protest activity having "little regard for the safety and security of our community".

"While the person who allegedly committed this crime does not live in the ACT, we have close working relationships with state police and they assisted in his identification, location and arrest," she said.

"This should serve as a warning to anyone protesting in the ACT.

"Peaceful protest activity is a person's right. However, if someone breaks the law they will be identified, arrested and placed before the court."

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