In 2006, while in Indonesia and six months pregnant, Abigail Haworth became one of the few journalists ever to see young girls being 'circumcised'. Until now she has been unable to tell this shocking story

It's 9.30am on a Sunday, and the mood inside the school building in Bandung, Indonesia, is festive. Mothers in headscarves and bright lipstick chat and eat coconut cakes. Javanese music thumps from an assembly hall. There are 400 people crammed into the primary school's ground floor. It's hot, noisy and chaotic, and almost everyone is smiling.

Twelve-year-old Suminah is not. She looks like she wants to punch somebody. Under her white hijab, which she has yanked down over her brow like a hoodie, her eyes have the livid, bewildered expression of a child who has been wronged by people she trusted. She sits on a plastic chair, swatting away her mother's efforts to placate her with a party cup of milk and a biscuit. Suminah is in severe pain. An hour earlier, her genitals were mutilated with scissors as she lay on a school desk.

During the morning, 248 Indonesian girls undergo the same ordeal. Suminah is the oldest, the youngest is just five months. It is April 2006 and the occasion is a mass ceremony to perform sunat perempuan or "female circumcision" that has been held annually since 1958 by the Bandung-based Yayasan Assalaam, an Islamic foundation that runs a mosque and several schools. The foundation holds the event in the lunar month of the Prophet Muhammad's birthday, and pays parents 80,000 rupiah (£6) and a bag of food for each daughter they bring to be cut.

It is well established that female genital mutilation (FGM) is not required in Muslim law. It is an ancient cultural practice that existed before Islam, Christianity and Judaism. It is also agreed across large swathes of the world that it is barbaric. At the mass ceremony, I ask the foundation's social welfare secretary, Lukman Hakim, why they do it. His answer not only predates the dawn of religion, it predates human evolution: "It is necessary to control women's sexual urges," says Hakim, a stern, bespectacled man in a fez. "They must be chaste to preserve their beauty."

I have not written about the 2006 mass ceremony until now. I went there with an Indonesian activist organisation that worked within communities to eradicate FGM. Their job was difficult and highly sensitive. Afterwards, in fraught exchanges with the organisation's staff, it emerged that it was impossible for me to write a journalistic account of the event for the western media without compromising their efforts. It would destroy the trust they had forged with local leaders, the activists argued, and jeopardise their access to the people they needed to reach. I shelved my article; to sabotage the people working on the ground to stop the abuse would defeat the purpose of whatever I wrote. Such is the tricky partnership of journalism and activism at times.

Yet far from scaling down, the problem of FGM in Indonesia has escalated sharply. The mass ceremonies in Bandung have grown bigger and more popular every year. This year, the gathering took place in February. Hundreds of girls were cut. The Assalaam foundation's website described it as "a celebration". Anti-FGM campaigners have proved ineffective against a rising tide of conservatism. Today, the issue is more that I can't not write about that day.

By geopolitical standards, modern Indonesia is an Asian superstar. The world's fourth-largest country and most populous Muslim nation of 240 million people, it is beloved by foreign investors for its buoyant economy and stable democracy. It is feted as a model of tolerant Islam. Last month, President Susilo Bambang Yudhoyono visited London to receive an honorary knighthood from the Queen in recognition of Indonesia's "remarkable transformation". Yet, as befitting an archipelago of 17,000 islands, it's a complicated place, too. Corruption and superstition often rule by stealth. Patriarchy runs deep. Abortion is illegal, and hardline edicts controlling what women wear and do are steadily creeping into local by-laws.

Although Indonesia is not a country where FGM is widely reported, the practice is endemic. Two nationwide studies carried out by population researchers in 2003 and 2010 found that between 86 and 100% of households surveyed subjected their daughters to genital cutting, usually before the age of five. More than 90% of adults said they wanted the practice to continue.

In late 2006, a breakthrough towards ending FGM in Indonesia occurred when the Ministry of Health banned doctors from performing it on the grounds that it was "potentially harmful". The authorities, however, did not enforce the ruling. Hospitals continued to offer sunat perempuan for baby girls, often as part of discount birth packages that also included vaccinations and ear piercing. In the countryside, it was performed mainly by traditional midwives – women thought to have shamanic healing skills known as dukun – as it had been for centuries. The Indonesian method commonly involves cutting off part of the hood and/or tip of the clitoris with scissors, a blade or a piece of sharpened bamboo.

Last year, the situation regressed further. In early 2011, Indonesia's parliament effectively reversed the ban on FGM by approving guidelines for trained doctors on how to perform it. The rationale was that, since the ban had failed, issuing guidelines would "safeguard the female reproductive system", officials said. Indonesia's largest Muslim organisation, the Nahdlatul Ulama, also issued an edict telling its 30 million followers that it approved of female genital cutting, but that doctors "should not cut too much".

The combined effect was to legitimise the practice all over again.

It is impossible to second-guess what kind of place holds mass ceremonies to mutilate girl children, with the aim of forever curbing their sexual pleasure. Bandung is Indonesia's third largest city, 180km east of the capital Jakarta. I had been there twice before my visit in 2006. It was like any provincial hub in booming southeast Asia: a cheerful, frenzied collision of homespun commerce and cut-price globalisation. Cheap jeans and T-shirts spilled out of shops. On the roof of a factory outlet there was a giant model of Spider-Man doing the splits.

Bandung's rampant commercialism had also reinvigorated its moral extremists. While most of Indonesia's 214 million Muslims are moderate, the 1998 fall of the Suharto regime had seen the resurgence of radical strains of Islam. Local clerics were condemning the city's "western-style spiritual pollution". Members of the Islamic Defenders Front, a hardline vigilante group, were smashing up nightclubs and harassing unmarried couples.

The stricter moral climate had a devastating effect on efforts to eradicate FGM. The Qur'an does not mention the practice, and it is outlawed in most Islamic countries. Yet leading Indonesian clerics were growing ever more insistent that it was a sacred duty.

A week before I attended the Assalaam foundation's khitanan massal or mass circumcision ceremony, the chairman of the Majelis Ulama Indonesia, the nation's most powerful council of Islamic leaders, issued this statement: "Circumcision is a requirement for every Muslim woman," said Amidhan, who like many Indonesians goes by a single name. "It not only cleans the filth from her genitals, it also contributes to a girl's growth."

It was early, before 8am, when we arrived at a school painted hospital green in a Bandung suburb on the day of the ceremony. Women and girls clad in long tunics were lining up outside to register. It was a female-only affair (men and boys had their own circumcision gathering upstairs), and the mood was relaxed and sisterly. From their sun-lined faces and battered sandals, some of the mothers looked quite poor – poor enough, possibly, to make the foundation's 80,000 rupiah cash handout as much of an enticement as the promise of spiritual purity.

Inside, I was greeted by Hdjella, 57, a teacher and midwife who would supervise the cutting. She was wearing a pink floral apron with a frilly pocket. She had been a traditional midwife for 32 years, she said, although, like most dukun, she had no formal training.

"Boy or girl?" she asked me, brightly. I was almost six months pregnant at the time.

"Boy," I told her.

"Praise Allah."

Hdjella insisted that the form of FGM they practised is "helpful to girls' health". She explained that they clean the genitals and then use sterilised scissors to cut off part of the hood, or prepuce, and the tip of the clitoris.

"How is this helpful to girls' health?" I asked. "It balances their emotions so they don't get sexually over-stimulated," she said, enunciating in schoolmistress fashion. "It also helps them to urinate more easily and reduces the bad smell."

Any other benefits? "Oh yes," she said, with a tinkling laugh. "My grandmother always said that circumcised women cook more delicious rice."

FGM in Indonesia is laden with superstition and confusion. A common myth is that it is largely "symbolic", involving no genital damage. A study published in 2010 by Yarsi University in Jakarta found this is true only rarely, in a few animist communities where the ritual involves rubbing the clitoris with turmeric or bamboo. While Indonesia doesn't practise the severest forms of mutilation found in parts of Africa and the Middle East, such as infibulation (removing the clitoris and labia and sewing up the genital area) or complete clitoral excision, the study found the Indonesian procedure "involves pain and actual cutting of the clitoris" in more than 80% of cases.

Hdjella took me to the classroom where the cutting would soon begin. The curtains were closed. Desks had been covered in sheets and towels to form about eight beds. Around each one, three middle-aged women wearing headscarves waited in readiness. Their faces were lit from underneath by cheap desk lamps, giving them a ghoulish glow. There were children's drawings and multiplication tables on the walls.

The room filled up with noise and people. Girls started to cry and protest as soon as their mothers hustled them inside. Rapidly, the mood turned business-like. "We have many girls to circumcise this morning, about 300," Hdjella shouted above the escalating din. As children were hoisted on to desks I realised with a jolt: this is an assembly line.

Hdjella led me to a four-year-old girl who was lying down. As the girl squirmed, two midwives put their faces close to hers. They smiled at her, making soft noises, but their hands took an arm and a leg each in a claw-like grip. "Look, look," Hdjella commanded, as a third woman leant in and steadily snipped off part of the girl's clitoris with what looked like a pair of nail scissors. "It's nothing, you see? There is not much blood. All done!" The girl's scream was a long guttural rattle, which got louder as the midwife dabbed at her genitals with antiseptic.

In the dingy, crowded room, her cries merged with the sobs and screeches of other girls lying on desks, the grating sing-song clucking of the midwives, the surreally casual conversational hum of waiting mothers. There was no air.

Outside in the courtyard, the festive atmosphere grew as girls and their mothers emerged from the classroom. There were snacks and music, and later, prayers.

Ety, 40, was elated. She had brought her two daughters, aged seven and three, to be cut. "I want them to be teachers. Being circumcised will bring them good luck," she said. Ety was a farmer who came from a village outside Bandung. "Daughters should be pure and obey their parents."

Neng Apip, 28, was smiling radiantly. She said she was happy her newly cut daughter Rima would now grow up into "a good Muslim girl". Rima, whose enormous brown eyes were oozing tears, was nine months old. Apip kissed her and gave her a rice cracker to suck. "Shh, shh, all better now," she cooed.

Tradition is usually about remembering. In the case of FGM in Indonesia it seems to be a cycle of forgetting. The act of cutting is a hidden business perpetrated by mothers and midwives, nearly all of whom underwent FGM themselves as young children. The women I met had little memory of being cut, so they had few qualms about subjecting their daughters to the same fate. "It's just what we do," I heard over and over again.

When the pain subsides, it is far from all better. The girls in the classroom don't know that removing part of their clitoris not only endangers their health but reflects deep-rooted attitudes that women do not have the right to control their own sexuality. The physical risks alone include infection, haemorrhage, scarring, urinary and reproductive problems, and death. When Yarsi University researchers interviewed girls aged 15-18 for their 2010 study, they found many were traumatised when they learned their genitals had been cut during childhood. They experienced problems such as depression, self-loathing, loss of interest in sex and a compulsive need to urinate.

I saw my interpreter, Widiana, speaking to Suminah, the 12-year-old who was the oldest girl there, and went to join them. Suminah said she didn't want to come. "I was shaking and crying last night. I was so scared I couldn't sleep." It was a "very bad, sharp pain" when she was cut, she said, and she still felt sore and angry. Widiana asked what she planned to do in the evening. "We will have a special meal at home and then read the Qur'an," said Suminah. "Then I will listen to my Britney Spears CD."

Back in Jakarta, an Indonesian friend, Rino, agreed to help me find out about the newborn-girl "package deals" at city hospitals. Rino phoned around Jakarta's hospitals. They told him he must see a doctor to discuss the matter. So we decided that is what we would do: since I was visibly pregnant, we'd visit the hospitals as husband and wife expecting our first baby. ("It's not necessary to bring your wife," Rino was told repeatedly when he rang back to book the appointments.)

We visited seven hospitals chosen at random. Only one, Hermina, a specialist maternity hospital, said it did not perform sunat perempuan. The other six all gave package prices, varying from 300,000 rupiah to 550,000 rupiah (£20-£36), for infant vaccinations, ear piercing and genital cutting within two months of birth.

Interestingly, the only doctor who argued against the procedure was a female gynaecologist from the largest Islamic government hospital, the Rumah Sakit Islam Jakarta. "You can have it done here if you wish," the doctor said with a sigh. "But I don't recommend it. It's not mandatory in Islam. It's painful and it's a great pity for girls."

Last month I spoke to Andy Yentriyani, a commissioner at Indonesia's National Commission on Violence Against Women. Yentriyani told me the problem is now worse than ever. Since the government's guidelines on FGM came into effect last year, more hospitals have started offering the procedure.

"Doctors see the guidelines as a licence to make money," she says. "Hospitals are even offering female circumcision in parts of Sumatra where there has never been a strong tradition of cutting girls."

"They are creating new demand purely for profit?"

"Yes. They're including it in birth packages. People don't really understand what they're signing up for." Nor do some medical staff, she adds. The new guidelines say doctors should "make a small cut on the frontal part of the clitoris, without harming the clitoris". But Yentriyani says that most doctors are trained only in male circumcision, so they follow the same principle of slicing off flesh.

Moreover, according to The Jakarta Post, the guidelines were rushed through partly in response to the deaths of several infant girls from botched FGM procedures at hospitals.

Likewise, Yentriyani says, the recent endorsement of FGM by some Islamic leaders has vindicated those carrying out mass cutting ceremonies, such as the Assalaam foundation. "Women are caught in a power struggle between religion and state as Indonesia finds a new identity," the activist explains. "Clamping down on morality, enforcing chastity, returning to so-called traditions such as female circumcision – these things help religious leaders to win hearts and minds."

Yentriyani and other Indonesian supporters of women's rights believe FGM can never be justified as a religious or cultural tradition. "Our government and religious leaders must condemn it outright as an act of violence, otherwise it will never end," she says. Her view is supported by organisations such as Amnesty International, which has called on Indonesia to repeal its guidelines allowing FGM. US Secretary of State Hillary Clinton has also weighed in, saying in February this year that, although many cultural traditions must be respected, female genital cutting is not one of them. "It is, plain and simply, a human rights violation," Clinton declared.

Suminah will be 18 now; a grown woman. She could well be married, or at least betrothed. Soon enough she will probably have her own kids. I hope she's forgotten her pain, but held on to her rage.