There is no firm prohibition of "FGM" in the Quran/Islam, but rather Islamic scripture can be used to justify such a practice and historically and unfortunately, this has been the case.

In concerning FGM, the four schools of sunni Islam hold-

"Shafi'is believe that it is either strongly encouraged or obligatory. Maalikis believe that it is recommended, not obligatory. Hanbalis believe that it is recommended, not obligatory. Hanafis believe that it is neither recommended, nor obligatory, but that it is a mere courtesy"

"Circumcision is prescribed for both males and females. The correct view is that circumcision of women is mustahabb but not obligatory." http://islamqa.info/en/45528

Aside from Indonesia featuring the practice of FGM (due of course to permission from Islam). It's interesting to note, there appears to be no cultural history of FGM in Indonesia, until the arrival of Islam in the 13th century...

"...Historical records suggest female circumcision in Indonesia started and became prevalent with the arrival of Islam in the 13th century as part of its drive to convert people to Islam. In islands of Indonesia, where partial populations converted to Islam in the 17th century, FGM has been prevalent in Muslim females only..."

https://en.wikipedia.org/wiki/Prevalence_of_female_genital_mutilation_by_country#Indonesia

The Indonesian government - with the help of various other child welfare charities and organisations - has renewed its attempt to prohibit the practice of FGM, despite facing opposition from religious/Muslim leaders...

http://www.reuters.com/article/us-indonesia-women-fgm-idUSKCN11R25Q