The family of the girl, identified as Soher, filed an official complaint, accusing the doctor who performed the operation of having caused her death.
The girl died on Thursday evening in a village in the Daqahliya governorate, north-east of Cairo.
Doctors and nurses in Egypt have been banned from performing procedures involving female genital mutilation (FGM) since 2007 following the death of two young girls after being subjected to such surgeries at public hospitals. The procedure was subsequently declared illegal in 2008.
The ban notwithstanding, poorer families continue to put youngsters at grave risk. According to national statistics, around 80 per cent of girls born to poor families become victims of FGM, as against only 30 per cent of girls from wealthy, educated backgrounds.