Nearly 20 years after the Rwandan genocide, Chris McGreal returns to Kibuye to meet the few Tutsis who survived – and some of the killers they are forced to live with as neighbours

Rwanda genocide 20 years on: 'We live with those who killed our families. We are told they're sorry, but are they?'

Lucie Niyigena's seven-year-old mind was a jumble of panic and confusion as she stepped over the brutalised, bleeding corpse of her grandfather and fled through the back door of her town's Catholic church. But, as Lucie remembers the terror nearly two decades later, she was driven by a single overwhelming urge – not to be separated from her mother in death.

"All I could think of was to be with my mother whatever happened," she says. "Even today, even though I want to get out of this place where so many terrible things happened, where there are still people who want them to happen again, where we can see the killers walking on the streets every day, I can never leave my mother."

Lucie was back at the church in Kibuye last month, gently washing the skulls of a few of the thousands of Tutsis killed there on a single day at the height of Rwanda's genocide in 1994. By some miracle – actually the decency of a few Hutu policemen, neighbours and a bank clerk who bravely if silently resisted the killing – she and her mother, Madalena Mukariemeria, stayed alive in an area of Rwanda where fewer than one in 30 Tutsis survived the genocide; in total, 800,000 Tutsis were lost to the killings led by a Hutu extremist government.

But survival demands a price. The mass killings have shaped Lucie's life, even though she was only a young child when the tide of death swamped Kibuye, a town of about 48,000 people on the edge of Lake Kivu at Rwanda's western border.

The trauma and fear that permeated her home in the early years are now mixed with flickers of hope, suspicion and resentment as the government – led by the former rebel leader, Paul Kagame, who put a stop to the genocide – seeks to construct a new Rwanda where the ideology of hatred is buried with the corpses of its victims.

Lucie is bound up in an unprecedented experiment in which an entire country has been pressed to atone, forgive and reconcile but never forget. That has meant the killers confessing and seeking mercy, and the survivors accepting those who murdered their families back from prison as neighbours. Meanwhile a new generation is being taught to reject the labels of Hutu and Tutsi, and find a common purpose in reconstructing Rwanda.

Some have embraced the role with vigour. In Kibuye, Hutu men who butchered entire families have offered heartfelt and detailed confessions that have prompted some survivors to set aside nearly unimaginable pain to embrace them as genuinely reformed. But scratch beneath the surface and Rwanda remains a country in shock.

A few yards from where Lucie is washing the skulls of the dead, a familiar-looking man is sweeping leaves from the mass grave of 4,500 Tutsis. He is short, with the same tightly cropped beard and haunted look I encountered in 1994 a few weeks after the church massacre, when the stench of the dead tossed just outside its walls still overwhelmed Sunday mass. Members of the congregation held cloths over their faces as they prayed, and then emerged to blame the Tutsis for their own deaths.

Lucie reminds me that the man's name is Thomas Kanyeperu and that he had been the church groundsman. She says he served nine years in prison for genocide. "He said he didn't do it," she tells me. "He said he saved Tutsis. Maybe he saved some Tutsis but he killed others. Even today he hates us. Ask him. You'll see."

The killing was so efficient in Kibuye and the surrounding province, where all but 8,000 of its 250,000 Tutsis were slaughtered, that it was known as the "pure genocide". That was in part due to the province's governor, Clément Kayishema, a doctor who took to the radio to urge Tutsis fleeing the marauding "interahamwe" gangs of Hutu extremists to shelter in the town's church.

They soon realised their mistake. The church was perched atop a small peninsula jutting into Lake Kivu. When the killing there began in earnest on 17 April 1994, there was nowhere to flee. Some Tutsis ran to the water only to be attacked by men in boats. The genocidaire tossed grenades into the lake just as they used explosives to catch fish.

In memoriam: skulls of those killed while seeking refuge in the church of Kibuye. Photograph: Andy Hall for the Observer

Those who lived were often saved by the decency of others. Lucie and her mother were inside the church when the interahamwe stormed in shooting and cutting away with machetes. As Tutsis fled through the back door some were killed on the spot, including Lucie's grandfather. Others were lined up for execution by men waving nail-studded clubs. By the end of the day 11,500 people had been murdered in and around the church. The next day another 10,000 Tutsis were killed in the football stadium.

But Lucie and her mother were rescued by policemen pretending they were taking them for execution. As they were marched away, Madalena heard a child crying among the vegetation. "We were furious because he was shouting and we thought it would bring the interahamwe," she tells me. "I thought to myself: 'Shut up child. Shut up or die.'"

A policeman rescued the boy. Only later did Madalena see that the child she wished dead was her eight year-old son, Maurice. Today he is an army officer.

Madalena's neighbours hid her and the children until it became too dangerous. After that the family burrowed deep into banana groves and hoped no one would find them. Over the coming weeks Madalena was captured, raped and saved from death by the bravery of a Hutu bank clerk who used his own money to bribe the interahamwe.

After the genocide, Madalena, who is now 62, took in six orphans from her extended family. One of them, Savera Mukasharango, was 15 when she committed suicide after coming face to face on the streets of Kibuye with the man who murdered her father. "After that she went and threw herself in the lake and drowned because of the pain of seeing him," says Madalena. "Today we are being asked to live with the people who killed our families. We are told they are sorry, they won't do it again. Some people believe that. I am not one of them."

A couple of years after the genocide I travelled through Kibuye with Tharcisse Karugarama, who was, at the time, the newly appointed prosecutor for the region. He was also adopting a young boy, orphaned and mutilated. The interahamwe had hacked the child's arms off. Over the years, Tharcisse rose from prosecutor to judge and then to head of the high court. He is now Rwanda's justice minister, who has had to contend with the daunting question of what to do with close to 150,000 accused genocidaire who a decade ago were packed into overcrowded, fetid prisons.

The survivors wanted justice for their murdered families but the government didn't have enough judges, lawyers or courtrooms to put the killers on trial. It faced the prospect of keeping them locked up without due process or freeing them without accounting for their crimes. Either way risked worsening the bitter legacy of genocide. President Kagame wanted to forge a new Rwandan identity devoid of Hutu and Tutsi. The answer lay in a form of traditional justice, known as gacaca, rejigged to serve as a mix of trial and local truth and reconciliation commissions.

The challenge was to get the killers to confess, in part to help the survivors discover how and where their loved ones died, but also as a counter by Hutu extremists in exile to deny the genocide. As gacaca rolled out, the government drew in the support of churches where preachers placed a heavy emphasis on biblical exhortations to confession and forgiveness. "All the talk of heaven and hell and redemption helped to start people talking," says Tharcisse. "And once a few talked, naming names, telling where the bodies were buried, who killed who, then the door was open."

Communities across the country elected 250,000 judges. Anyone was permitted to speak at the hearings, against or for a defendant. The accused were encouraged to confess their own crimes and name other genocidaire in return for reduced sentences and often swift release from Rwanda's grim prisons. The floodgates opened. "We learned the truth about what happened. Who did what, how, when, where," says Tharcisse. "One of the successes of gacaca is everything was told. Nothing very significant is unknown."

Louis Rutaganira learned the fate of his family at a gacaca hearing. It prompted him to embrace reconciliation with an enthusiasm in direct proportion to his suffering. The last Louis saw of his wife, Marie Claire, was as she was hacked with machetes outside Kibuye's Catholic church. He never again saw three of his four children, then aged six to 12. Louis survived by hiding under dead bodies piled among the pews. He calculates that 86 of his relatives died in and around the church. Today he runs a clothes and textile shop in Kibuye's newly built market, and has remarried.

Louis was sceptical when the government began pushing forgiveness and reconciliation. "After 2004, the authorities told us every day to work very hard and forget about the past," he says. "It was very difficult. We were told to put national reconciliation first. But it was hard when these people who killed our loved ones would not even tell us how they died."

No place of refuge: the church in Kibuye where 11,500 Tutsi men, women and children were massacred by Hutu extremists. Photograph: Andy Hall for the Observer

Then came gacaca, and from the killers' confessions Louis learned who stripped his wife naked and cut off all of her limbs, leaving her to bleed to death. "It was shocking to hear the one who killed my wife saying he was the one who killed my wife. The ones who killed my children also confessed. They were very sincere. Nobody forced them to speak.

"I accepted their apologies," Louis continues. "It is painful but necessary. The killers are our neighbours now."

Zacharia Niyorurema also found himself in front of a gacaca court, accused of murdering his Tutsi neighbours, including a man who was once his school teacher. After nearly a decade in prison, Zacharia asked the teacher's son, Odile Kabayita, for forgiveness. "I told him: 'I killed your father,' and asked to be pardoned," he says. "Kabayita for some time said he would think about it. Then he said he accepted to forgive me personally but told me to go to gacaca to tell the whole story." The court accepted Zacharia's confession and released him from prison in 2006. Today he works on a building site.

Odile heads the survivors' association in Kibuye. It initially opposed gacaca as being too soft on the perpetrators, but was persuaded of its worth once the trials revealed details of where many lost bodies had been buried – the sites of long-overgrown mass graves, entire families dumped down hillside latrines. Odile says he forgave Zacharia as a contribution to reconstructing Rwanda. In turn Zacharia helped build Odile a new house.

"I'm a good Christian and I accepted Zacharia's confession," Odile tells me. "We must do this for our country. It is painful and I can't say they are all 100% sincere. But if we compare to where we're coming from it's a very big improvement. We're happy when we see someone come and confess they killed someone. And we forgive them."

Over a decade, gacaca courts considered allegations about 1.3m people involving nearly 2m crimes. "The victims got justice, the perpetrators got justice," says Tharcisse.

Much has changed over the past two decades. Kibuye, once a dilapidated backwater isolated by bad roads, now has a highway to the capital, Kigali, multi-storey banks, offices and a cultural museum. Tourist hotels dot the lake shore. New street lamps in the colours of the national flag are popping up over town.

Ten years ago, the most prominent building was the prison, packed with accused genocidaire in pink uniforms, that stood close to the entrance to the town as a symbol of its nightmare. The prison is gone now, replaced by a park. The church has been cleaned up, its bullet-riddled stained glass windows and roof replaced, although the stonework still carries evidence of the crime. The memorials to the dead are ordered and tended, even if more graves are found all the time.

Mostly the pain of the past is carried inside. But occasionally it screams out. The annual genocide memorial commemoration last month was marked with a candlelit march from the stadium to the church. Amid the singing of soulful songs – "Let us remember people who died in the genocide. Don't be discouraged. Keep on hoping for a better future. Be brave, don't be angry" – came the wails as survivor after survivor broke down in distress.

Not everyone views gacaca as the success the government claims. It has delivered up confessions and information but too often the guilty give a "just obeying orders" defence, leaving Tutsis wondering if some might not do it all again if told to. Lucie's mother, Madalena, became a regular witness at gacaca. "I was naming the killers we saw killing our families," she explains. "We were hated especially by those people who were out of prison. Even now they hate us for giving evidence against them. During the night they throw stones at my house. They kill my livestock, my cows, my bananas. They won't come and buy from my shop. They use bad words.

"Some of the killers tell the truth of what happened," Madalena says of gacaca. "But others did not tell the truth." Her complaints go against the official line, and Cyriaque Niyonsaba, political leader of the sector that includes Kibuye, dismisses her as a crank. "She is not behaving well. She's putting about stories that are not true," he tells me when we meet. "Even the other survivors tell her to shut up."

Madalena acknowledges that. "I can't keep quiet. I don't regret it since it's the truth. It's a way of supporting those who perished. There are some survivors who don't want to talk. They come to me and say, 'Are you talking? Just keep quiet.' But I can't."

On the day Lucie is washing the skulls, Thomas Kanyeperu, the former church caretaker who served nine years in prison for genocide, has been given a day's work helping to tidy the site ready for the annual genocide memorial week. I introduce myself to Thomas and explain that I met him at the church in 1994. He misunderstands and quickly says he wasn't in Kibuye during the genocide. I remind him I spoke to him by the bell tower not long after the massacres. He changes his story and says he was there, but is a hero for saving the lives of Tutsis.

Facing the future: Thomas Kanyeperu, who served nine years in prison for his part in the massacre. Photograph: Andy Hall for the Observer

"There is friendship between the people now," says Thomas. "Reconciliation is very good. The government has done well on housing. They are giving me a new house. The one I have is very old." Then doubt creeps into his voice. "I support national reconciliation. But there's still some who can't understand what national reconciliation is." Who? "Individuals looking after their own interests," replies Thomas.

It becomes apparent he's talking about the survivors, and that Thomas thinks only Hutus are doing the reconciling. "Sometimes the survivors say things that aren't true. Some survivors claim they lost many things, even what they didn't have before the war. A survivor would come and say there was a house here and it was destroyed but there was never any house. They are just looking for money. Sometimes the government looks after them first. That's where the hatred comes from."

I ask what hatred he means. "Some people still hate them," says Thomas. Does this happen a lot? "Yes, a lot," he says.

Thomas offers no real sympathy for the genocide's victims but says he learnt a lesson from the killing. "You find out killing is not a solution. They killed thinking they would get something and they found out it only brought misery." He says "they" I notice, but the gacaca court found he shared some responsibility. "I shouldn't have been in prison," he replies. "It was a very hard life. I fell sick. I was very lucky to survive, and it didn't affect me only. My family suffered a lot."

I tell Lucie and Sister Genevieve, a nun who is helping her wash the bones of the dead, that Thomas says he's innocent. They both laugh. "He killed," says the nun. Do his denials bother them? "What do you expect?" asks Lucie.

Even Louis Rutaganira, the enthusiast for reconciliation, says Thomas is not alone in his attitude. "There are many people who accepted their crimes in order to get out of prison. They didn't accept their crimes from their hearts. It is a surprise to see. The survivors are willing to live with these people but these people don't want to live with us."

It's supposed to be different with the two- thirds of Rwandans under the age of 25 who have little or no direct memory of the genocide. In school, they are encouraged to reject the concepts of Hutu and Tutsi and to find common purpose in building a new Rwanda. "Most of my friends are Hutu," says Lucie. "We can't talk about the past. They want to forget the genocide. We want to remember. Even the younger generation are getting bad ideas from their parents. They still have the idea of Hutu and Tutsi. Some of them recognise that Kagame has done good things, but not all."

Lucie laughs off the idea that she would ever marry a Hutu, for all the talk of intermarriage as evidence of reconciliation. "It's too difficult to marry him. Even if I know his family, I don't think his family can accept me. From the side of my family, I don't think it would work. It would be difficult between our families because people still remember.

"I'm not very hopeful for the future," she adds. "We live with what we live with. I don't think about the future because it's not easy."

Kagame's push for reconciliation is intended to make another genocide unthinkable. The political line from Cyriaque Niyonsaba is that Rwanda has changed enough that the slaughter will not be repeated. "I'm really confident that this will never happen again," he tells me. "Every Rwandan is ashamed at what happened – how people killed their neighbours, their sister-in-laws, total strangers. The people have been shocked. Not only the Tutsi suffered, also those who fled to Congo and died. All of us suffered from the genocide."

"If someone came and told me to kill I wouldn't do it," agrees Zacharia. "I have seven children. My first born is 24. One day I sat with my children and told them what I did. I teach them not to do what I did because of these politicians."

But Madalena is not persuaded. She has two portraits of Kagame on her living room wall. She regards him as her saviour and protector. A few years back, Madalena told me that if Kagame ever leaves power – the constitution requires him to step down as president in 2017 – she would head straight to Uganda. Now she says that she doesn't want Lucie to wait.

"It would be better if she left now," she says. "Kagame can't go to every house teaching people how to reconcile. He speaks on the radio and some people listen but he cannot go house to house making people understand. Those who killed don't regret what they did. If they get the means, they could do it again."

Lucie hesitates. "It's better for people who left this place," she agrees. But then she looks across at Madalena. "I can't leave her alone," she says.