Moutia Elzahed, the wife of jailed Islamic State extremist Hamdi Alqudsi, allegedly remained seated in front of District Court Judge Audrey Balla multiple times in November and December 2016, saying she only stood for Allah.

But the niqab-wearing Muslim woman stood for magistrate Carolyn Huntsman at Sydney's Downing Centre Local Court on Monday, after being charged with disrespectful behaviour in court.

The 49-year-old allegedly refused to stand while suing the state and federal governments over alleged police violence during a raid on her Sydney home.

She lost that case but has since won the right to appeal.

Elzahed's lawyer on Monday said the current case raised several constitutional and jurisdictional issues. He also raised concerns about how the charges were laid.

Defence barrister David Hume said the NSW attorney-general referred the matter to the solicitor-general which was a "more political" exercise of power that effectively interfered with the judiciary.

"When the executive starts coming along and deciding when and how behaviour in the courtroom should be regarded, that presents a grave risk of conflict between two different branches of government," he said.

Mr Hume also said Solicitor-General Michael Sexton SC didn't consider whether the case was appropriate, desirable and in the public interest.

But crown prosecutor David Kell argued the authority to start proceedings was valid and didn't require "that the public interest somehow be imported into it".

Six witnesses are due to testify over the three-day hearing. CCTV footage and court transcripts are expected to be tendered as evidence.

The Australian National Imams Council in December said Islamic defendants have no faith-based reason not to stand before a judge or uncover their faces while giving testimony.

Australian Associated Press