By the standards of the Emberá, Colombia’s second largest indigenous group after the Wayuu, Karina is a fairly modern-minded woman. Having spent much of her childhood in Bogotá, the Colombian capital, she navigates big cities easily. She speaks relatively fluent Spanish in addition to her native tongue and, although she married at the usual age of 14, she’s on the pill, preferring not to have children until she’s older.

But there’s one subject on which Karina, 17, is a staunch traditionalist. When she does have children, if she has a girl, the baby’s clitoris will be cut in the long-held tradition of the Emberá, the only ethnic group in Latin America known to practise female genital mutilation (FGM).

“I couldn’t leave the girl just like that without taking it off because later she will be embarrassed,” says Karina, reflecting the strongly held belief among the Emberá that if a clitoris is not cut it will become a penis.

FGM is widely known to be practised in 28 African countries and in parts of Asia and the Middle East.

Known among the Emberá as curación, the origins of the practice in Colombia are the subject of various theories. One holds that it was adopted from African communities brought as slaves to the continent, and there is anecdotal evidence that some Afro-Colombian communities still practise it.

Another is that a hermaphrodite was once born into the community and midwives acted to prevent the possibility of a girl developing into a man. “It is considered a defect that must be corrected,” says Patricia Tobón, an Emberá lawyer who has worked with women in her community to help them understand FGM and try to prevent it. “They try to remove the masculine side of girls.”

The practice came to light among the Emberá after the deaths of two newborn girls in 2007 in Pueblo Rico. Focusing on the two municipalities in which the girls died, public health officials, human rights defenders and the UN scrambled to find the origin of the practice and stop it.

But there are about 230,000 Emberá in Colombia, and the group’s presence stretches from the border with Panama to the frontier with Ecuador.

The revelation that FGM is practised stunned many in the Emberá community. Men had no idea their daughters were cut at birth and many women – oblivious to the fact that they had been cut as babies – only learned the truth with the birth of their first girl. “It was a closely guarded secret,” says Tobón.

Oliva Cheché’s first child was a girl. She barely had time to hold her in her arms before an elder woman from her community in the Alto Andágueda region of Chocó province took the baby away. When she brought her back swaddled in blankets, the girl was screaming uncontrollably. Cheché didn’t know what had happened and didn’t ask. She was only 15 and this was her first child. When her second daughter was born several years later, the same thing happened.

By the time she had her third daughter, she knew the truth and refused to hand her over to anyone. “I said I didn’t care about tradition, I didn’t want my girls to suffer,” she says.

There are no official statistics on FGM in Colombia. “We don’t know the magnitude of the problem in the country,” says Dana Barón of the UN Population Fund (UNFPA) in Bogotá. “Girls can die and are buried quietly, and no one finds out,” she says. “But one achievement is that the Emberá have recognised it as a problem.”

Officially, Emberá leaders say the practice has been banned. After several years of anthropological research backed by the UNFPA and an education campaign among midwives and other women, national indigenous authorities prohibited curación in 2012 and called for punishment in wooden stocks for anyone practising it.

But Karina says that in her community the stocks are for those who talk about the practice to outsiders, which is why she asked not to be identified with her real name.

Anti-FGM campaigners first spoke to women about the sexual pleasure they were missing by not having a clitoris. “Culturally, this made no sense to them,” says Nancy Millan, a sociologist who coordinated the investigation into the practice alongside an education programme designed to eradicate it. “We focused, instead, on the danger to the girls’ health and the risk of death.”

But the campaign may be a victim of its own success. Since midwives have now learned to sterilise themselves and their tools, fewer girls appear to be dying. So Karina considers that the problem is being solved. “If they use the right herbs, it doesn’t get infected and the girls don’t get sick,” she says.

The last girl to arrive at the hospital in Mistrató suffering from the effects of FGM did not benefit either from sterilisation or “the right herbs”. A 15-year-old mother brought her 20-day-old daughter to the emergency room with a high fever and jaundice. The girl’s clitoris and inner labia had been excised, and the wound was covered in pus.

“The girl’s mother said that she’d been born that way,” says Dr Diego Pereira, pointing to a photograph of the girl’s wounds on his computer. Social workers now show the picture to women as a warning of what could happen. But such overt images and language can backfire.

When the UN education programme began, trained Emberá nurses started teaching women about general anatomy, explaining what is inside the head and the thorax. “When the nurses started talking about genitals, the women got angry, kicked them out, and warned 23 other communities not to allow the nurses to speak to the women,” says Tobón.

Public focus on their secret practices has put many Emberá leaders on the defensive. In Mistrató, leaders say they have decided not to allow further investigations into the issue in their communities and not to talk about it with outsiders.

Midwives, who know they face sanctions for the practice, flatly deny ever having done it. “I haven’t killed anyone,” are the first words spoken by Feliciana Nacavrea, 67, a midwife, when asked about the practice.

At a recent meeting of midwives and female leaders in the Emberá community of Bacorí, only a few of the women spoke openly with outsiders about curación – and they seemed uncomfortable. But they do talk openly about the education programme, which was called Emberá Wera (Embera Woman).

Maria Fanny Zamora, who sits on the regional indigenous council, says the relationship between men and women has changed as Emberá women, who are used to carrying the bulk of the workload and suffer beatings by their husbands, are told of their rights. “Because of the workshops we have become empowered,” she says.

UN funding for the workshops dried up in 2011, and while Colombian public health officials continue to promote the eradication of FGM and the UN is supporting a smaller project, these programmes lack the initial drive.

“The project ended and we didn’t get to all the communities in our reservation. Curación continues in the more remote communities,” says Elisa Onogama, a midwife in Pueblo Rico who now believes that FGM serves no purpose in Emberá culture. “But we have to convince all Emberá women so that our girls will no longer be in danger.”