The woman is due to give evidence for the prosecution in the fraud trial of a Muslim college director Anwar Sayed.
Perth District Court Judge Shauna Deane said that she did not consider it appropriate that the witness give evidence with her face covered.
She however stressed that she was not making a decision -which was making a legal precedent- but it was simply her ruling in the circumstances.
Defence lawyers had earlier raised concerns that the burqa would not help the jury to read the woman's facial expressions.
Defence lawyer Mark Trowell had said that the woman's wish to wear the burqa was a "preference she has".It's not an essential part of the Islamic faith. If she was in an Islamic court she would be required to remove it," News.com.au quoted Trowell, as saying.
On the other hand, Prosecutor Mark Ritter had told the court that the woman would feel uncomfortable without the burqa.
"It goes beyond stress . . . it would have a negative impact," he said.
He said that the woman had worn the burqa since the age of 17, and went without it only before her family and male blood relatives. (ANI)