They brought in the bodies one by one, laying them down on a white sheet concealed behind a flimsy black curtain. Among them was a man, probably in his 20s, his head twisted leftward, the skull dented on one side and cracked open on the other. The others also had fatal head injuries that stained the sheet crimson. The first flies began settling on the five corpses.

In the courtyard outside, voices were raised in anger and bewilderment. Mothers in pink and purple hijabs sobbed and wailed and a middle-aged man, possibly unused to naked shows of emotion, sat and gently wept. Finally the iron gate of the mosque was thrown open and the mourners surged forward to gaze at the dead. An imam, donning a plastic smock over his white robe, prepared to wash them while another man began cutting cotton shrouds for the day's burials.

The macabre scene in an area known as PK5 has become almost commonplace in Bangui, the humid and decaying capital of the Central African Republic (CAR), where Muslims are under siege. It has also been played out in towns and villages in the west of the country, redrawing the demographic map.

Muslims came here to trade in the early 19th century and made up 15% of the CAR's population a year ago, but since then untold thousands have been killed or displaced or have fled to neighbouring countries. The UN said last week that while 130,000 to 145,000 Muslims normally lived in the capital, Bangui, the population had been reduced to around 10,000 in December and now stood at just 900.

Amnesty International has called it "ethnic cleansing" and warned of a "Muslim exodus of historic proportions".

As Africa prepares to mark next month's 20th anniversaries of the Rwandan genocide and the end of South African apartheid, what is happening in this long-neglected state is a reminder that forgiveness and reconciliation are easy words but hewn from rock over generations. Christian militias freely admit that theirs is an exercise in vengeance, an eye for an eye, and they will not stop until they have "cleaned" the country of Muslims. On Monday, UN human rights investigators in CAR announced they would investigate reports of genocide.

The seeds were sown in March last year when the Seleka, a largely Muslim rebel group, seized Bangui in a coup, installed the country's first Muslim president, Michel Djotodia, and terrorised the majority Christian population, killing men, women and children. In response, predominantly Christian forces known as the anti-balaka (balaka means machete in Sango, the local language) launched counterattacks against the Seleka and perceived Muslim collaborators.

International pressure forced Djotodia to step down in January and soon the Seleka, who once strutted confidently about the capital, were retreating north where they continue to persecute Christians. But as the anti-balaka gained the advantage elsewhere, village after village lost its Muslim population, their homes looted and mosques razed to the ground. The turning of the tide has left many Muslims feeling bitter towards French peacekeepers and the new president, Catherine Samba-Panza, a Christian.

A girl walks through the rubble of demolished Muslim homes in the Miskine district of Bangui. Photograph: Siegfried Modola/Reuters

Bangui neighbourhoods such as PK5, once thriving with Muslim businesses, now resemble ghost towns. On a recent Tuesday afternoon, hundreds of market stalls and small shops were empty and deserted as a body lay in the road and gun-toting African peacekeepers patrolled in an armoured vehicle. Down side streets there were vehicles piled high with personal belongings. It is estimated that the Muslim population has dropped from around 7,000 to just 1,000 here.

At the mosque where the five bodies lay, there was rage, coupled with confusion over whether the anti-balaka or Burundian peacekeepers were responsible for the deaths. "It is happening every day," said Abdouraman Saudi, 45, who has lost numerous businesses. "If you're Muslim and you try to leave PK5, you're a dead man. It's a prison."

He vowed: "For me, it's finished. From today, we will not be the victims because we will attack the Christians. We are going to defend ourselves. From today with the international community, we don't care. We are not protected by them so we will attack them also."

In another largely Muslim neighbourhood, PK12, families camp out in grass and mud with buckets, carpets, mattresses, discarded rubbish, cooking pots over charcoal fires and a constant fear of lobbed grenades. Convoys that try to get out of here must run the gauntlet of taunting Christian mobs. In one incident, a Muslim who fell from a vehicle was summarily lynched. In another, five children suffocated in an overcrowded truck and were found dead when the convoy arrived at Bangui's military airport.

Ibrahim Alawad, 55, a lawyer, pointed to a trench and fresh burial mounds and said he had buried a 22-year-old student hours earlier. The area's population had shrunk from 25,000 people six months ago to 2,700 today, he said, while four mosques had been destroyed. "They're not killing the Muslims, they're sweeping them. Imagine someone wants to kill you, roast you on the fire and eat you. It's the hell of the hell. There are no living conditions here."

French peacekeepers stood by at a near checkpoint but there was growing Muslim hostility towards them too. "Our problem is the French," Alawad said. "They are the white anti-balaka. It's like Rwanda, they want to do it again, but we won't let them."

No amount of Muslim suffering appears to elicit mercy from the anti-balaka, who believe they are meeting a fitting punishment for the crimes of the Seleka. Dr Jean Chrysostome Gody, director of the country's sole paediatric hospital, which is supported by Unicef, recalled: "I saw mothers whose children had been killed or injured and they had hate in their heart."

Members of the anti-balaka militia train in the Boeing neighbourhood of Bangui. Photograph: Fred Dufour/AFP/Getty Images

As the anti-balaka responded, he added, children were no longer caught in the crossfire but deliberately targeted. "There were bullets in the heads and chests of children. It's not possible they were there by accident. It's as if people are trying to finish off another race. It's about extreme revenge and it's brutal."

One anti-balaka base is nicknamed "Boeing" because it is within close sight and sound of air traffic at Bangui airport. In a clearing shaded by trees amid modest mudbrick houses, six of the militia men sprawled on two squashy sofas. One wore a Barcelona football shirt with the name Messi on the back; another carried a bow and arrow; several had machetes. When a French patrol comes to disarm them every few days, they hide their weapons in the bush.

Forgiveness is not in the lexicon here. Sebastien Wenezoui, 32, a civil engineer, said he helped instigate the anti-balaka after his parents and brothers were killed by the Seleka and their house torched. "I was shocked. Today you can see my feelings in what I'm doing now. I had to express myself. If you were me, would you be comfortable with those things?"

Asked if he felt this justified the killing of innocent women and children, Wenezoui replied: "For me it's a response to what the Seleka have done. They started killing our children and wives and destroyed our homes. Revenge is good sometimes and bad sometimes. But we have to do it."

Wenezoui expressed no regrets about the Muslim exodus. "I'm not sad at all because when Seleka took power the Muslims, who were our best friends, were the ones destroying the houses and killing people. It's a kind of lesson. They acted like betrayers so they have to go and learn something and come back with respectful behaviour."

Yet sitting with Wenezoui and his colleagues was a Muslim: Ibrahim Amadou, 22, who said he joined the anti-balaka after his wife, three children, parents and seven siblings were shot dead by the Seleka. He still prays on Fridays but does so at home because fellow Muslims would recognise him at a mosque.

"I cannot give all the details of what I'm doing," said Amadou, wearing an array of animal skin and leather charms around his neck and shoulders that he believes make him invisible to enemies. "I'm working for the country. A soldier is a soldier: he cannot give his secrets."

A member of the anti-balaka holds a grenade and a sabre at a checkpoint in Pissa, CAR. Photograph: Sia Kambou/AFP/Getty Images

Nearby, there is no sign of respite for tens of thousands of people squatting outside the international airport, fearful of going home in a city where the Red Cross said more than 10 people were killed in February, some found with their genitals stuffed in their mouths, and where grenades are said to be available at street markets for 250 CFA (31p) and Kalashnikov rifles for 10,000-15,000 CFA (£12-£18). There is a threat of the country splitting in two, and a fully fledged UN peacekeeping mission may be required to stop it.

In the town of Boali, 60 miles to the north, the Catholic priest Xavier-Arnauld Fagba went from house to house and into the bush to offer Muslims sanctuary in his church. "When the Muslims were attacked, the people didn't help them," said Fagba, 31, who became a priest four months ago. "That's when I decided to look for them and bring them here. I did it in the name of my faith. My faith asks me to transcend the most difficult obstacles."

Nearly 700 people took up his offer and moved into the church.

But most local Christians disagreed with Fagba's courageous stand and one day his car was surrounded by anti-balaka armed with knives and machetes. He got out to show that he did not fear them and, just then, their commander called off the assault.

In another incident last month, more than 300 anti-balaka surrounded the church and opened fire through its thinly protected walls. Fagba hurled himself to the ground and shouted at everyone else to do the same – and no one was killed or injured. He says some 30 bullet holes can still be seen in the church walls.

The Muslims held prayers every Friday in the grounds of the 54-year-old church, and cleaned it early on Sunday mornings for the Christian service, which some even attended.

But rebuilding bridges is a slow and painful process. Local officials tried to organise a peace march in which Muslims and Christians would walk together through the town, but when the Muslims arrived, the anti-balaka refused. "It's very sad because I thought it was the beginning of peace," Fagba said.

On 1 March a convoy of trucks protected by African peacekeepers evacuated the inhabitants of the church, and took them to safety in Cameroon, leaving Boali with no Muslim inhabitants.