The rainy season is over and the Niger Delta is lush and humid. This southern edge of West Africa, where Nigeria's wealth pumps out of oil and gas fields to bypass millions of its poorest people, is a restless place. In the small delta state of Akwa Ibom, the tension and the poverty has delivered an opportunity for a new and terrible phenomenon that is leading to the abuse and the murder of hundreds, perhaps thousands, of children. And it is being done in the name of Christianity.

Almost everyone goes to church here. Driving through the town of Esit Eket, the rust-streaked signs, tarpaulins hung between trees and posters on boulders, advertise a church for every third or fourth house along the road. Such names as New Testament Assembly, Church of God Mission, Mount Zion Gospel, Glory of God, Brotherhood of the Cross, Redeemed, Apostalistic. Behind the smartly painted doors pastors make a living by 'deliverances' - exorcisms - for people beset by witchcraft, something seen to cause anything from divorce, disease, accidents or job losses. With so many churches it's a competitive market, but by local standards a lucrative one.

But an exploitative situation has now grown into something much more sinister as preachers are turning their attentions to children - naming them as witches. In a maddened state of terror, parents and whole villages turn on the child. They are burnt, poisoned, slashed, chained to trees, buried alive or simply beaten and chased off into the bush.

Some parents scrape together sums needed to pay for a deliverance - sometimes as much as three or four months' salary for the average working man - although the pastor will explain that the witch might return and a second deliverance will be needed. Even if the parent wants to keep the child, their neighbours may attack it in the street.

This is not just a few cases. This is becoming commonplace. In Esit Eket, up a nameless, puddled-and-potholed path is a concrete shack stuffed to its fetid rafters with roughly made bunk beds. Here, three to a bed like battery chickens, sleep victims of the besuited Christian pastors and their hours-long, late-night services. Ostracised and abandoned, these are the children a whole community believes fervently are witches.

Sam Ikpe-Itauma is one of the few people in this area who does not believe what the evangelical 'prophets' are preaching. He opened his house to a few homeless waifs he came across, and now he tries his best to look after 131.

'The neighbours were not happy with me and tell me "you are supporting witches". This project was an accident, I saw children being abandoned and it was very worrying. I started with three children, then every day it increased up to 15, so we had to open this new place,' he says. 'For every maybe five children we see on the streets, we believe one has been killed, although it could be more as neighbours turn a blind eye when a witch child disappears.

'It is good we have this shelter, but it is under constant attack.' As he speaks two villagers walk past, at the end of the yard, pulling scarfs across their eyes to hide the 'witches' from their sight.

Ikpe-Itauma's wife, Elizabeth, acts as nurse to the injured children and they have called this place the Child Rights and Rehabilitation Network, a big name for a small refuge. It has found support from a charity running a school in the area, Stepping Stones Nigeria, which is trying to help with money to feed the children, but the numbers turning up here are a huge challenge.

Mary Sudnad, 10, grimaces as her hair is pulled into corn rows by Agnes, 11, but the scalp just above her forehead is bald and blistered. Mary tells her story fast, in staccato, staring fixedly at the ground.

'My youngest brother died. The pastor told my mother it was because I was a witch. Three men came to my house. I didn't know these men. My mother left the house. Left these men. They beat me.' She pushes her fists under her chin to show how her father lay, stretched out on his stomach on the floor of their hut, watching. After the beating there was a trip to the church for 'a deliverance'.

A day later there was a walk in the bush with her mother. They picked poisonous 'asiri' berries that were made into a draught and forced down Mary's throat. If that didn't kill her, her mother warned her, then it would be a barbed-wire hanging. Finally her mother threw boiling water and caustic soda over her head and body, and her father dumped his screaming daughter in a field. Drifting in and out of consciousness, she stayed near the house for a long time before finally slinking off into the bush.Mary was seven. She says she still doesn't feel safe. She says: 'My mother doesn't love me.' And, finally, a tear streaks down her beautiful face.

Gerry was picked out by a 'prophetess' at a prayer night and named as a witch. His mother cursed him, his father siphoned petrol from his motorbike tank and spat it over his eight-year-old face. Gerry's facial blistering is as visible as the trauma in his dull eyes. He asks every adult he sees if they will take him home to his parents: 'It's not them, it's the prophetess, I am scared of her.'

Nwaeka is about 16. She sits by herself in the mud, her eyes rolling, scratching at her stick-thin arms. The other children are surprisingly patient with her. The wound on her head where a nail was driven in looks to be healing well. Nine- year-old Etido had nails, too, five of them across the crown of his downy head. Its hard to tell what damage has been done. Udo, now 12, was beaten and abandoned by his mother. He nearly lost his arm after villagers, finding him foraging for food by the roadside, saw him as a witch and hacked at him with machetes.

Magrose is seven. Her mother dug a pit in the wood and tried to bury her alive. Michael was found by a farmer clearing a ditch, starving and unable to stand on legs that had been flogged raw.

Ekemini Abia has the look of someone in a deep state of shock. Both ankles are circled with gruesome wounds and she moves at a painful hobble. Named as a witch, her father and elders from the church tied her to a tree, the rope cutting her to the bone, and left the 13-year-old there alone for more than a week.

There are sibling groups such as Prince, four, and Rita, nine. Rita told her mum she had dreamt of a lovely party where there was lots to eat and to drink. The belief is that a witch flies away to the coven at night while the body sleeps, so Rita's sweet dream was proof enough: she was a witch and because she had shared food with her sibling - the way witchcraft is spread - both were abandoned. Victoria, cheeky and funny, aged four, and her seven-year-old sister Helen, a serene little girl. Left by their parents in the shell of an old shack, the girls didn't dare move from where they had been abandoned and ate leaves and grass.

The youngest here is a baby. The older girls take it in turn to sling her on their skinny hips and Ikpe-Itauma has named her Amelia, after his grandmother. He estimates around 5,000 children have been abandoned in this area since 1998 and says many bodies have turned up in the rivers or in the forest. Many more are never found. 'The more children the pastor declares witches, the more famous he gets and the more money he can make,' he says. 'The parents are asked for so much money that they will pay in instalments or perhaps sell their property. This is not what churches should be doing.'

Although old tribal beliefs in witch doctors are not so deeply buried in people's memories, and although there had been indigenous Christians in Nigeria since the 19th century, it is American and Scottish Pentecostal and evangelical missionaries of the past 50 years who have shaped these fanatical beliefs. Evil spirits, satanic possessions and miracles can be found aplenty in the Bible, references to killing witches turn up in Exodus, Deuteronomy and Galatians, and literal interpretation of scriptures is a popular crowd-pleaser.

Pastor Joe Ita is the preacher at Liberty Gospel Church in nearby Eket. 'We base our faith on the Bible, we are led by the holy spirit and we have a programme of exposing false religion and sorcery.' Soft of voice and in his smart suit and tie, his church is being painted and he apologises for having to sit outside near his shiny new Audi to talk. There are nearly 60 branches of Liberty Gospel across the Niger Delta. It was started by a local woman, mother-of-two Helen Ukpabio, whose luxurious house and expensive white Humvee are much admired in the city of Calabar where she now lives. Many people in this area credit the popular evangelical DVDs she produces and stars in with helping to spread the child witch belief.

Ita denies charging for exorcisms but acknowledges his congregation is poor and has to work hard to scrape up the donations the church expects. 'To give more than you can afford is blessed. We are the only ones who really know the secrets of witches. Parents don't come here with the intention of abandoning their children, but when a child is a witch then you have to say "what is that there? Not your child." The parents come to us when they see manifestations. But the secret is that, even if you abandon your child, the curse is still upon you, even if you kill your child the curse stays. So you have to come here to be delivered afterwards as well,' he explains patiently.

'We know how they operate. A witch will put a spell on its mother's bra and the mother will get breast cancer. But we cannot attribute all things to witches, they work on inclinations too, so they don't create HIV, but if you are promiscuous then the witch will give you HIV.'

As the light fades, he presents a pile of Ukpabio's DVDs. Mistakenly thinking they are a gift, I am firmly put right.

Later that night, in another part of town, the hands of the clock edge towards midnight. The humidity of the day is sealed into the windowless church and drums pound along with the screeching of the sweat-drenched preacher. 'No witches, oh Lord,' he screams into the microphone. 'As this hour approaches, save us, oh Lord!'

His congregation is dancing, palms aloft, women writhe and yell in tongues. A group moves forward shepherding five children, one a baby, and kneel on the concrete floor and the pastor comes among them, pressing his hands down on each child's head in turn, as they try to hide in the skirts of the woman. This is deliverance night at the Church of the True Redeemer, and while the service will carry on for some hours, the main event - for which the parents will have paid cash - is over.

Walking out into the night, the drums and singing from other churches ring out as such scenes are being repeated across the village.

It is hard to find people to speak out against the brutality. Chief Victor Ikot is one. He not only speaks out against the 'tinpot' churches, but has also done the unthinkable and taken in a witch to his own home. The chief's niece, Mbet, was declared a witch when she was eight. Her mother, Ekaete, made her drink olive oil, then poison berries, then invited local men to beat her with sticks. The pastor padlocked her to a tree but unlocked her when her mother could not find the money for a deliverance. Mbet fled. Mbet, now 11, says she has not seen the woman since, adding: 'My mother is a wicked mother.'

The Observer tracked down Mbet's mother to her roadside clothing stall where she nervously fiddled with her mobile phone and told us how her daughter had given her what sounded very much like all the symptoms of malaria. 'I had internal heat,' she says, indicating her stomach. 'It was my daughter who had caused this, she drew all the water from my body. I could do nothing. She was stubborn, very stubborn.' And if her daughter had died in the bush? She shrugged: 'That is God's will. It is in God's hands.'

Chief Victor has no time for his sister-in-law. 'Nowadays when a child becomes stubborn, then everyone calls them witches. But it is usually from the age of 10 down, I have never seen anyone try to throw a macho adult into the street. This child becomes a nuisance, so they give a dog a bad name and they can hang it.

'It is alarming because no household is untouched. But it is the greed of the pastors, driving around in Mercedes, that makes them choose the vulnerable.'

In a nearby village The Observer came across five-year-old twins, Itohowo and Kufre. They are still hanging around close to their mother's shack, but are obviously malnourished and in filthy rags. Approaching the boys brings a crowd of villagers who stand around and shout: 'Take them away from us, they are witches.' 'Take them away before they kill us all.' 'Witches'.

The woman who gave birth to these sorry scraps of humanity stands slightly apart from the crowd, arms crossed. Iambong Etim Otoyo has no intention of taking any responsibility for her sons. 'They are witches,' she says firmly and walks away.

And by nightfall there are 133 children in the chicken coop concrete house at Esit Eket.

· Watch the video: Child witches in Africa