Judge Peter Murphy said he would not allow the 21-year-old defendant to stand trial in the veil, which only revealed her eyes, because a different person could go into the dock pretending to be her.
"It is necessary for this court to be satisfied that they can recognise the defendant. While I obviously respect her right to dress in any way she wishes, certainly while outside the court, the interests of justice are paramount,” he said.
During a hearing at Blackfriars Crown Court in London on Thursday, Murphy said he could not accept a plea from a person whose identity he was unable to ascertain.
He stressed that "the principle of open justice" could not be subject to the religion of the defendant.
"It would be easy for someone on a later occasion to appear and claim to be the defendant. The court would have no way to check on that," he said.
According to The Daily Telegraph, the Muslim woman from Hackney in east London, whose identity cannot be revealed for legal reasons, says she cannot remove the veil in front of any men because of her religion.
She is facing allegations of intimidating a witness in Finsbury Park, north London, in June.
The woman's barrister, Claire Burtwistle, told the court she was not prepared to lower her veil at all while men were in the courtroom.
"In front of women, it is not an issue. It is simply men that she will not allow to see her face," she said.
Burtwistle suggested that she, a female police officer or a female prison guard could identify the defendant and confirm to the court that it was the same person.
Prosecutor Sarah Counsell said the police officer in charge of the case was content that he recognised the defendant while she was in the burqa.
But the judge rejected these suggestions and adjourned the case till September 12, when the court will hear arguments over whether the woman should remove her veil.
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