The directions come after a string of courtroom incidents where Islamic defendants refused to stand before judges in court - citing their faith in defence of their actions.
The wife of terrorist recruiter Hamdi Alqudsi, Moutia Elzahed, was the first person in New South Wales to be charged with disrespectful behaviour 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.
Written in collaboration with the Judicial Commission of NSW to establish a better understanding of the Muslim community, an explanatory note released by the Australian National Imams Council said Muslims have been told there is no prohibition on them standing before a judge or magistrate.
The ANIC said their document, entitled Explanatory Note on the Judicial Process and Participation of Muslims, is intended to "give practical guidance and explanation to members of the Australian Muslim community of the etiquette and behaviours expected of persons engaging in the judicial processes so that they may act consistently with these without compromising their religious beliefs".
It is also intended to "provide information to judicial officers on Islamic concepts and practices as they relate to matters which may be raised in connection with Muslims participating in the court processes".
"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.
