"This will give doctors a new motivation to circumcise [girls] because now they can say the Ministry of Health approves of this, and the Indonesian Ulamas’ Council approves of it," Jurnalis Uddin, doctor and lecturer at Yarsi University in Jakarta, told IRIN.
Though FGM/C was banned in 2006, two of Indonesia’s Muslim organizations, including the largest and mostly moderate Nahdlatul Ulama, ultimately condone the practice advising "not to cut too much", and, as a result, many continue to perform the procedure.
By directing health professionals not to cut a girl’s genitals but to "scrape the skin coveringthe clitoris, without injuring the clitoris", the Ministry of Health stands by the regulations, passed in June, as a medically safe form of FGM/C representing an effort to further regulate the illegal practice and protect women.
But recent uproar has questioned this reasoning. Others are concerned the guidelines could well be misinterpreted as an endorsement of the procedure, combined with an enticement for doctors to encourage the practice, Uddin said.
"I think that doctors will use these guidelines to make money from circumcision," Uddin said, adding that Indonesia’s poorly regulated medical practitioners often viewed medicine as a business.
FGM/C is typically done at birth, or before a girl is five years old and in the past was often performed by local healers, called dukun, or by birth attendants. Traditionally, FGM/C was mostly "symbolic" with a small cut on the clitoris, or rubbing the clitoris with tumeric root, making it less invasive than other types of FGM/C.
However, Uddin, who conducted an Indonesia-wide survey of FGM/C practices in 2009, said he had found that when medical practitioners performed the procedure, there was a trend toward more extensive cutting of the clitoris.
Dozens of Indonesian groups continue to call for the Ministry to revoke the guidelines.
"This gives a justification for health practitioners to damage women’s bodies," said Frenia Nababan, spokeswoman for the Indonesian Family Planning Association. She added, "We fear it will increase control of women’s bodies by the state and religious groups."
Amnesty International, is one of more than 100 signatories to a letter stating that the guidelines should be revoked partially on the grounds of Indonesia’s child protection laws, as well as the government’s commitment to the international Convention on the Elimination of All Forms of Discrimination against Women (CEDAW), signed by Indonesia in 1984.
Experts say there has been increasing support for the practice from Muslim groups since the downfall of authoritarian leader Suharto in 1998, resulting in greater religious and political freedom, known as "Reformasi".
"Before Reformasi [FGM/C] was mostly done on an individual basis, but since Reformasi, it has been done in mass events," said Siti Musda Mulia, an academic specializing in Islamic studies, who initially conducted research on the process during the Suharto era, and has conducted follow-up research since 1998.
Uddin found Indonesia-wide FGM/C had not increased dramatically since the Suharto era; however in some areas, such as Bandung, West Java, there was an increasing tendency to perform it, even among moderate Muslims.
Across Indonesia approximately 12 percent of female babies born in hospitals, birthing centres or assisted by government midwives have been circumcised, a figure that excludes FGM/C procedures done outside such facilities, Uddin said.
FGM/C remains a controversial practice, with debated origins. Religious experts say it is a foreign cultural practice not sanctioned in any of Islam’s religious texts.
Even a scratch or small cut on the clitoris is a dangerous procedure to perform on infants, say medical practitioners. Long-term consequences include bladder and urinary tract infections, as well as cysts and infertility.
The Ministry of Health argues it is not "legitimizing or legalizing" FGM/C with its standards but only trying to make the practice less risky by encouraging trained health professionals rather than traditional healers to perform the procedure.
"It is feared that community members who want to circumcise female babies will therefore go to traditional healers for this procedure, and it will increase the number of [medical] complications. If this procedure is done by health professionals, then it has to be done in accordance with the ministerial instruction 1636, and this will guarantee the protection of the female reproductive system," the Ministry stated in response to national criticism.