Prime Minister Anthony Albanese on Thursday announced the royal commission which will examine the nature and prevalence of anti-Semitism and religiously-motivated extremism.
Former High Court judge Virginia Bell will lead the inquiry which is expected to report back by the one-year anniversary of the December 14 mass shooting.
At the same time, criminal proceedings against the sole surviving alleged gunman Naveed Akram, 24, on murder and terrorism charges will progress through the courts.
His father Sajid Akram was shot dead by police on the day of the massacre when 15 people were killed while celebrating Hannukah at the beach and more than 40 others were injured.
The royal commission could proceed without prejudicing the case against Naveed, criminal law professor Tyrone Kirchengast told AAP.
However, certain steps would have to be taken to let prosecutors continue without interference, by shielding certain information from the public through redacted documents or private hearings, he said.
Other matters relating to sensitive policing issues or national security would also be kept confidential, the University of Sydney professor added.
"The royal commissioner will need to make decisions," Prof Kirchengast said.
"Some of those decisions may sit uncomfortably but those decisions will need to be made for a fair trial or for national security or a combination of both."
He said it was highly unlikely Naveed Akram's defence team would apply for a permanent stay of the criminal case because of the royal commission.
Such a move would be extraordinary, extreme and unprecedented, he told AAP.
Mr Albanese on Thursday said the royal commission would not prejudice the criminal proceedings because he had faith in the qualified Ms Bell and her experience in criminal law.
The terms of reference included a requirement not to interfere with the ongoing prosecution, he said on Friday.
"What you need to do is to make sure that all of those legal measures are got precisely right," he said on Nine's Today Show.Â
"We have done that."
