Dr Babatunde Osotimehin told the BBC that the custom was a human rights abuse and needed to end immediately.
More than 200 million women and girls around the world have undergone the procedure, where parts of the female genitals are removed.
The UN estimates a further three million are at risk of being mutilated.
Dr Osotimehin said: "There is absolutely no reason to cut anybody, and it seemed to us that it is part of the gender imbalance that has always existed in these communities which are based on patriarchy. I think it's child abuse."