The doctor went to the three girls' house after their Egyptian father told them they would receive a coronavirus "vaccination", Egypt's prosecutor-general said. The girls, aged under 18, were drugged and the doctor cut their genitals.
Female genital mutilation (FGM) was made illegal in 2008 in Egypt but remains prevalent.
A coronavirus vaccine currently does not exist although global trials to develop one are under way.
The girls told their mother, who is divorced from their father, about the procedure and she notified authorities. Girls suffer unbearable pain. Meanwhile, the doctor has been charged.
Doctors can be imprisoned for up to seven years if they are found guilty of the procedure.
PHOTO: Female circumcision in the world. We warn you about very unpleasant views!
Despite being outlawed in many parts of the world, the ritual is still practised globally.
The procedures alter or injure female genital organs for non-medical reasons, and often involve the removal or cutting of the labia and clitoris.
The UN estimates that 200 million women and girls alive today have undergone some form of genital mutilation.
In Egypt, it is widespread in both Christian and Muslim communities, and is often justified for cultural or religious reasons but is rooted in the desire to control a woman's sexuality.
As much as 87% of Egyptian women and girls aged 15-49 have undergone FGM, according to a 2016 survey by the UN Children's Fund.
It can cause lasting physical and mental trauma, including chronic infections, menstrual problems, infertility, pregnancy and childbirth complications.
Every year, many young women across the world die after this procedure, it violates the rights of women and children, so rights defenders around the world are fighting against this procedure.