There is a Roman Catholic priest at a medieval church an hour's drive from Paris who has been indicted by a United Nations court for genocide, extermination, murder and rape in Rwanda.

Father Wenceslas Munyeshyaka was notorious during the 1994 genocide of 800,000 Tutsis for wearing a gun on his hip and colluding with the Hutu militia that murdered hundreds of people sheltering in his church. A Rwandan court convicted the priest of genocide and sentenced him in absentia to life in prison. The International Criminal Tribunal for Rwanda spent years trying to bring him to trial.

But the Catholic church in France does not see any of this as a bar to serving as a priest and has gone out of its way to defend Munyeshyaka.

It's not an isolated case. After the genocide, a network of clergy and church organisations brought priests and nuns with blood on their hands in Rwanda to Europe and sheltered them. They included Father Athanase Seromba who ordered the bulldozing of his church with 2,000 Tutsis inside and had the survivors shot. Catholic monks helped him get to Italy, change his name and become a parish priest in Florence.

After Seromba was exposed, the international tribunal's chief prosecutor, Carla Del Ponte, accused the Vatican of obstructing his extradition to face trial. The Holy See told her the priest was "doing good works" in Italy. Another Rwanda priest taken on in Italy is facing charges of overseeing the massacre of disabled Tutsi children.

The Vatican's reluctance to confront the murderers in its midst is rooted in its refusal to face up to the church's complicity in mass murder. But as Rwanda marks the 20th anniversary of the genocide, the time has come for Pope Francis to follow his own lead on paedophile priests and apologise for the part played by the clergy in turning churches into extermination centres. The Vatican should accompany a plea for forgiveness with a calling to account of priests complicit in the killing.

For two decades, the Vatican has maintained that, while individual clergy were guilty of terrible crimes, the church as an institution bears no responsibility. The Holy See would prefer the world to focus on the more than 200 priests and nuns killed in the genocide. But, while there is no doubt there were courageous members of the clergy, many Tutsi survivors regard the church as allied with the killers and culpability as beginning at the very top of the Catholic hierarchy in Rwanda.

Archbishop Vincent Nsengiyumva was so closely attached to the Hutu power structure that for nearly 15 years he sat in the ruling party's central committee as it implemented the policies of discrimination and demonisation that laid the ground for genocide. His political affiliations left him well placed to at least try to urge the regime to stop the killing in 1994 and to have been a strong moral voice in public against the slaughter. Instead, he was incapable even of calling the massacres a genocide let alone condemning the politicians and military officers leading them. The archbishop became so compromised that witnesses said he stood by as Tutsi priests, monks and a nun were taken to be murdered.

Many of Nsengiyumva's bishops and priests were apologists for the killers by falsely trying to pin blame for the massacres on Paul Kagame's mostly Tutsi rebel army. That sent a message to the murderers that the church was not going to judge them. Some openly said that God had abandoned the Tutsis.

The Organisation for African Unity's report on the genocide described the church in Rwanda as carrying a "heavy responsibility" for failing to oppose, and even promoting, ethnic discrimination. It said the church offered "indispensable support" to the Hutu regime during the killing and described church leaders as playing "a conspicuously scandalous role" in the genocide by failing to take a moral stand against it.

"This stance was easily interpreted by ordinary Christians as an implicit endorsement of the killings, as was the close association of church leaders with the leaders of the genocide," the report said.

I went to see Munyeshyaka at his church in Gisors a few months ago. He denies the charges against him and defiantly defends carrying a gun during the genocide. He also remains unapologetically aligned with groups that keep alive the ideology that underpinned the genocide.

Clearly Munyeshyaka is not going to apologise for his part in Rwanda's tragedy. All the more reason for the pope to acknowledge that the Catholic church failed in Rwanda in 1994, and continues to do so by protecting such priests.

• Chris McGreal's Chaplains of the Militia, on the role of churches during the genocide in Rwanda, is out now from Guardian Shorts. Visit guardianshorts.com to read an extract and find out more