The health ministry's step cancelled a 1996 provision to the law which had permitted circumcision "in situations of illness" should doctors advise it.
The measure to outlaw the practice entirely came after a girl died while undergoing the procedure at a private medical clinic last week.
Budour Ahmed Shaker died in the southern province of Minya, south of Cairo, after she was given a heavy dose of anaesthetic, security sources said.
She had been taken to the clinic by her mother but died before she could be transferred to a hospital.
The practice, which affects both Muslim and Christian women in Egypt, is believed to have begun in the time of the pharoahs.