The directions come after a string of courtroom incidents where Islamic defendants refused to stand before judges in court - citing their faith in defense of their actions.
The wife of terrorist recruiter Hamdi Alqudsi, Moutia Elzahed, was the first person in NSW to be charged with disrespectful behavior after she refused to stand before District Court judge Audrey Balla late in 2016. She was trying to sue over alleged police violence during a raid on her Revesby home.
But in an explanatory note released by the Australian National Imams Council, Muslims have been told there is no prohibition on them standing before a judge or magistrate.
"Standing up for the Magistrate or Judge is a sign of respect to the court. This sign of respect is also reflected in the teaching of Islam," the note read.
Women were also allowed to uncover their faces while giving testimony in court, the note directed.
"It is not contrary to Sharia law for the Magistrate or Judge (male or female) to look at her in order to know or identify who she is, make assessments as to credibility where this is an issue and protect the rights of all concerned," it said.