A Sydney court started on Friday the trial of the first female genital mutilation case in New South Wales in which three people were accused of performing circumcision on two girls aged 6 and 7 in 2012.

Charged at the Parramatta Local Court were the mum of the two girls, Sheikh Shabbir Vazin, 53, and a 69-year-old retired nurse who performed the procedure.

Their lawyers insist the three did not breach the state's law, claiming the nick or cut done on the organs of the two girls failed to meet the legal definition of mutilation. They said there must be circumcision and tissue removal for the procedure to be considered mutilation.

But Magistrate Roger Brown rejected their argument, stressing that "all non-medical mutilation is prohibited ... Any nick or cut to the clitoris will amount to mutilation."

He reminded the three that female genital mutilation is banned even for religious or cultural reasons used to justify the practice.

He pointed out that while a small cut on the clitoris may seem like a small incident, if the same procedure would be performed on male genitals. Many men would balk from the procedure.

The case resumes on June 20.