Captive audience … Papuan boys at the Daarur Rasul Islamic boarding school, outside Jakarta, behind locked gates.

Captive audience … Papuan boys at the Daarur Rasul Islamic boarding school, outside Jakarta, behind locked gates. Photo: Michael Bachelard

Johanes Lokobal sits on the grass that cushions the wooden floor of his little, one-room house. He warms his hands at a fire set in the centre. From time to time a pig, out of sight in an annex, squeals and slams itself thunderously against the adjoining wall.

The village of Megapura in the central highlands of Indonesia's far-eastern province of West Papua is so remote that supplies arrive by air or by foot only. Johanes Lokobal has lived here all his life. He does not know his exact age: "Just old," he croaks. He's also poor. "I help in the fields. I earn about 20,000 rupiah [$2] per day. I clean the school garden." But in a hard life, one hardship particularly offends him. In 2005, his only son, Yope, was taken to faraway Jakarta. Lokobal did not want Yope to go. The boy was perhaps 14, but big and strong, a good worker. The men responsible took him anyway. A few years later, Yope died. Nobody can tell Lokobal how, nor exactly when, and he has no idea where his son is buried. All he knows, fiercely, is that this was not supposed to happen.

"If he was still alive, he would be the one to look after the family," Lokobal says. "He would go to the forest to collect the firewood for the family. So I am sad."

Heavy learning … boys and girls at Daarur Rasul.

Heavy learning … boys and girls at Daarur Rasul. Photo: Michael Bachelard

The men who took Yope were part of an organised traffic in West Papuan youth. A six-month Good Weekend investigation has confirmed that children, possibly in their thousands, have been enticed away over the past decade or more with the promise of a free education. In a province where the schools are poor and the families poorer still, no-cost schooling can be an irresistible offer.

But for some of these children, who may be as young as five, it's only when they arrive that they find out they have been recruited by "pesantren", Islamic boarding schools, where time to study maths, science or language is dwarfed by the hours spent in the mosque. There, in the words of one pesantren leader, "They learn to honour God, which is the main thing." These schools have one aim: to send their graduates back to Christian-majority Papua to spread their muscular form of Islam.

Ask the 100 Papuan boys and girls at the Daarur Rasul school outside Jakarta what they want to be when they grow up and they shout, "Ustad! Ustad! [religious teacher]."

Watch and learn … students watch a performance of singing, dancing and wrestling.

Watch and learn … students watch a performance of singing, dancing and wrestling. Photo: Michael Bachelard

In Papua, particularly in the Highlands, the issues of religious and cultural identity are red-hot. Census data from over the past four decades shows that the indigenous population is now matched in number by recent migrants, largely Muslims, from other parts of Indonesia. The newcomers' domination of the economy, particularly in the western half of the province, effectively marginalises the original inhabitants. This immigration means that indigenous Papuans have a real - and realistic - fear of becoming an ethnic and religious minority in their own country. Stories of people taking away their children adds an emotive edge and has the potential to inflame tensions in an already volatile region.

For about 50 years, a separatist insurgency has been active in Papua and hundreds of thousands have died in their efforts to gain independence for the province. Christianity, brought by Dutch and German missionaries, is both the faith of a vast majority of the indigenous population, and a key part of their identity. Islam actually has an even longer history in Papua than Christianity, but it's of a gentler kind than what's preached in Java's increasingly hardline mosques and it's still, for the moment at least, the minority religion. But when the pesantren children return from Java, their faith has changed. "They become different persons," Papuan Christian leader Benny Giay, tells me. "They have been brainwashed".

The schools insist they recruit only students who are already Muslims, but it's clear they are not too fussy. At Daarur Rasul, I quickly found two little boys, Filipus and Aldi, who were mualaf - brand new converts from Christianity. One radical Islamic organisation, Al Fatih Kafah Nusantara (AFKN), makes no bones about its intention to convert, and to use religion for political ends. Leader Fadzlan Garamatan says AFKN has brought 2200 children out of Papua as part of his program of nationalistic "Islamicisation". "When [Papuans] convert to Islam, their desire to be independent reduces," says Fadzlan on AFKN's internet page.

Johanes Lokobal says his son died after being taken to an Islamic school.

Johanes Lokobal says his son died after being taken to an Islamic school. Photo: Michael Bachelard

In restive West Papua, the movement and conversion of young children is politically explosive. We were warned a number of times not to chase the story. It's never reported in the Indonesian press. The chief of the Indonesia government's Jakarta-based Unit for the Acceleration of Development in Papua and West Papua, Bambang Darmono, downplays it as just one of "many issues in Papua", and the Religious Affairs Ministry's director of pesantrens, Saefudin, says he has never heard of it. But my efforts to trace the life and death of one Papuan boy has revealed that the trade goes on. And, in the service of grand religious and political aims, sometimes young lives are broken.

Elias Lokobal smiles to himself when he talks about the feisty little stepbrother he lost, but when talk turns to Amir Lani, his expression darkens. Lani is a local cleric in Megapura and the other villages surrounding the highland capital, Wamena. It was in about 2005 when he and Aloysius Kowenip, the police chief from the nearby town of Yahukimo, began approaching families to recruit their children. The pair worked to take five boys from vulnerable families in each of five villages and transport them to Java for education. Kowenip, a Christian, says it was his idea to "help" the children, and that the funding came from "the local government and an Islamic organisation" whose name he could not remember. He says he sought out children with only one living parent because "nobody guided them".

Young Yope was one such boy. Although he had a stepmother, his natural mother had died. Neither Lani nor Kowenip ever visited Yope's father, Johanes Lokobal, to explain their scheme. It still rankles. "These people should ask permission from the parents," Lokobal says. Instead, they asked young Yope himself, who was enthusiastic about this adventure. Some friends had gone the previous year and he was keen to join them.

School spirit … students at Daarur Rasul perform chants in praise of prophet Muhammed.

School spirit … students at Daarur Rasul perform chants in praise of prophet Muhammed. Photo: Michael Bachelard

When it came time for Yope to depart, it happened in a flash, stepbrother Elias recalls. "I went to school, and when I came back there was no one home."

Andreas Asso was part of the same group. Now a shy young man scrabbling a living in Jayapura, the capital of West Papua, he was perhaps 15 at the time. Like Yope, Andreas had only one parent. His father was dead and, though his mother was alive, he was living with his stepmother. Like Yope, he was approached directly. "They asked if I wanted to pursue my study in Jakarta for free," Andreas says. "The police chief never spoke to my stepmum but he spoke to my uncle, the brother of my father, and he agreed. I was born Christian and I'll always be Christian. The police chief just said we'd be put in a boarding house ... If he had told us it would be a pesantren, none of us would have wanted to go."

When the day came to leave, Andreas says a group of 19 boys were loaded into an Indonesian air force Hercules C-130 aircraft in Wamena. By some accounts, the youngest of them was just five. The plane was crewed by men in uniform. It has been difficult to verify whether the military was officially involved, but a former Papuan army chief says civilians are permitted to buy cheap tickets to fly on military aircraft as part of the military's "corporate social responsibility". "We didn't speak to the soldiers," Andreas recalls. "We were afraid."

It took two days for the plane to reach Jakarta and, "we were not fed or offered drinks. A few, especially the little ones, got sick ... a few vomited," Andreas says. "When they came to my village, I thought I wanted to go. But when I was in the aeroplane, all I was thinking was, 'I want to go back to my village.' " When they landed in Jakarta, the boys were driven about three hours to their new home - the Jamiyyah Al-Wafa Al-Islamiyah pesantren, high on the slopes of the volcano, Mount Salak, behind the regional city of Bogor. The head of the Al-Wafa school's foundation, Harun Al Rasyid, remembers Andreas Asso and the boys from Wamena, and the men who brought them, Amir Lani and Aloysius Kowenip, whom he knows as "Aloy". The two men had come and "offered the students" in 2005, he recalls. "Aloy was ambitious in politics, and bringing children to my pesantren was a way to improve his standing or image in society," Al Rasyid says.

Andreas Asso's account and his differ on many points but they concur on one: the boys from the village in the wild highlands of Papua simply did not fit in. "It wasn't like a real school because in school they have classes," Andreas says. "In this one, we just went to a big mosque and all we learnt about was Islam, just reading the Koran. Sometimes they slapped us on the face, beat us with a wooden stick. They just told us we Papuans were black, we have dark skin."

The food and education at Al-Wafa were free but the religion was strict. It has Yemeni teachers and Saudi funding and its website describes it as Salafi sholeh, or "pious Salafi". Its purpose: "Setting up a cadre of preachers and people who can call others to Islam." Andreas insists that, like him, some of the other boys were Christians, and that the head of the school changed five of their names to make them sound more Islamic - allegations Al Rasyid denies. For his part, Al Rasyid says the Papuans were an unruly rabble who exhausted the teachers "because their cultural background was different".

He says the boys urinated and defecated on the school grounds and stole the crops of neighbouring farmers. He admits punishing them by "scolding" and hitting them "with rattan on the foot". About two or three months after they arrived, one sickly boy, Nison Asso, died.

"He was 10 years old," says Andreas. "He was already sick in Wamena but ... he passed away. The body is still there in Bogor because the boarding school didn't have the money to send the body back, though his parents wanted the body sent back." Al Rasyid will not comment on Nison's fate. After less than a year, it was clear to both the boys and the school that the experiment was failing, so Amir Lani was summoned. Andreas says he pleaded with Lani to take him home, but was refused. Instead, Lani took them to Jakarta to another Papuan man, Ismail Asso, who himself had been an imported student whose name was changed. Ismail told the boys there was not enough money to return them to Papua. Their parents, it seems, were never consulted.

Some of the students were found a new pesantren in Tangerang, near Jakarta. Later they were to be expelled from there, too, because, according to Ismail Asso, "These children were already bad children in Papua." But Andreas stayed out of school and instead teamed up with another boy, Muslim Lokobal, "who was also a Christian but was given the name 'Muslim' ". The pair went to make their own way in the big city.

A persistent problem in researching this story has been pinning down details - names, times and ages. Names have been changed, roots erased, and village children rarely know their own age. The tragic end to Yope Lokobal's story suggests, however, that he may be the same boy whom Andreas Asso knew as Muslim Lokobal.

Andreas says that one night Muslim got drunk. There is no eyewitness to what happened next, and it's the subject of five or more differing, second-hand accounts. Andreas's is the most gruesome. "On the way back to the boarding house, Muslim made trouble with the local people, so they beat him up and killed him. They put his body inside the boarding house. And because they hated him, they took out one of his eyes and put a bottle in the eye socket." Does this awful scene describe Yope's death? Or was Muslim a different boy?

Back in the village of Megapura, they can shed little light. "There was a call from Jakarta to the mosque at Megapura, and the people from the mosque gave us the news," Johanes Lokobal recalls. "There was no explanation about how Yope died." Says stepbrother Elias: "It was 2009 or 2010. We just held a mourning ceremony at home, praying." Nobody knows where Yope's body is buried.

The rest of the boys from that Hercules would be in their early 20s by now. Last time Andreas Asso heard from them, they were in Jakarta as little better than beggars - "street singers or working in public transport - the drivers' assistant, collecting the passengers," he says. It's not known how many groups of children Amir Lani and Aloysius Kowenip organised to take away. Teronce Sorasi, a mother from Wamena, says she was approached in 2007 or 2008 by "the police chief", who asked her to send her daughter, Yanti, who was then five, and her son, Yance 11, to Jakarta, even though "we are a Christian family". "I said, 'no' because my husband had just passed away and we were still mourning," Sorasi says.

Amir Lani still lives in a villa in the hills near Megapura. According to Elias, whenever people ask him about the lost boys of Wamena, "he just avoids them". When I reach Aloysius Kowenip by telephone, he boasts of his scheme. "If any one of them has become somebody, then, as a Papuan, I am proud of that." But when asked about those who died or failed, Kowenip abruptly ends the call. A few days later, his friend Ismail Asso phones in a fury, then issues two threats via SMS. "I remind you ... not to dig out information about the Muslims of Wamena," he writes, otherwise the "provocative foreign journalist" will be "deported from Indonesia", or "axed, killed by the [people of] Wamena".

Internal transportation of children has a long and dishonourable history in Indonesia. Around 4500 children were removed from East Timor over the 24-year Indonesian occupation to serve, in the words of author Helene Van Klinken in her book Making Them Indonesians, a "proselytising Islamic faith", and to bind the region closer to Jakarta. Children, she wrote, were chosen because they were "impressionable and easily manipulated to serve political, racial, ideological and religious aims".

Papua has been a target in the past, too. In 1969, former president Suharto proposed transferring 200,000 children of the "backward and primitive Papuans, still living in the stone age" to Java for education. Another Saudi-backed group, DDII, used to bring children from both East Timor and Papua. And today, AFKN, which is linked to the thuggish, hardline Islamic Defenders Front (FPI), is actively seeking children to recruit.

Daarur Rasul is half pesantren, half building site in a satellite city of Jakarta called Cibinong. Here, 100 boys from the lowlands in Papua's western half crowd up to the heavy bars of a gate to greet us. The gate is locked because, according to one member of staff, "they like to escape". Forty or so girls live downstairs with more freedom of movement. School principal Ahmad Baihaqi insists he teaches moderate Islam, and the children are at least seven, but some look younger. He doesn't deny they are locked up, but says it is only during study hours "to put discipline on them".

In 2011, four boys did escape and claimed not only that they'd been forced to work on the construction site, but that at the school, they had been left hungry, given unboiled water to drink and were taught only Islam, Indonesian language and maths. Baihaqi insists the boys exaggerate, saying they had been "naughty" from before they arrived. He agrees that sometimes his students do work on the construction site, but says they enjoy it. The boys' lessons begin at 4am with prayers. School continues, with breaks and an afternoon nap, until 9pm, during which there are seven hours of prayer and Koran reading and only 3 1/2 hours for "natural sciences, social sciences, reading and writing".

Baihaqi says he recruits new students in Papua every year and swears parents give their consent. But the children only travel home every three years. They don't miss their parents, he says, and the parents knowingly agree to the arrangement.

Arist Merdeka Sirait, the head of Indonesia's non-government child protection group Komnas PA, says separating children for that long "means erasing their cultural roots", particularly if their names and religion are also changed. "It is very dangerous," he adds. But Indonesia's powerful Religious Affairs Ministry has no problem with it. It's encouraged, in fact, says pesantren division director Saefudin, because, "The longer you stay [in a pesantren], the more blessing you'll get."

The Indonesian government's Child Protection Commission, KPAI, is also sanguine. Deputy chairman Asrorun Ni'am, who is also a senior member of the Fatwa Council of the MUI, the government's Islamic advisory body, was more worried about the "religious sentiment" we might stir up by writing the story. "It's against all efforts to build harmonious atmosphere," he warned us.

The law is clear. The UN Convention on the Rights of the Child, to which Indonesia is a party, says children should not be separated from their families for whatever reason, even poverty. And Indonesia's Child Protection Act includes a five-year jail penalty for those who convert a child to religion different from their family's. In West Papua, religious leaders have little doubt that removing children is part of a broader effort to overwhelm the indigenous population; "It is Indonesia's long-term project to make Papua an Islamic place," says the head of the province's Baptist church, Socratez Yoman. "If Jakarta wants to educate Papuan children," says Christian leader Benny Giay, "why don't they build schools in Papua?"

We could not confirm if the government of Indonesia or its agencies were active in the movement of children. But some organisations have high level support. AFKN is funded by zakat (Islamic alms) delivered through the charitable arm of state-owned Indonesian bank BRI; Aloysius Kowenip talked of "local government" funding; Daarur Rasul's donors include "some police officers and military officers" acting personally, and at least one group was moved by a military plane.

Perhaps, like the well-documented movement of children in East Timor, the Papuan operation has no government endorsement but enjoys quiet consent at high levels of Indonesian society. Andreas Asso survived to tell his tale, but remains furious at how he was duped into leaving his highland home, then abandoned to his fate.

"I could have had an education there in Wamena. Some of my friends who stayed have graduated from school ... My dream job is to become a policeman. But I look back, and I've achieved nothing."