'When I give food to the poor, they call me a saint. When I ask why they are poor, they call me a communist." So said the Brazilian archbishop Dom Hélder Câmara. His adage exposes one of the great fissures in the Catholic church, and the emptiness of the new pope's claim to be on the side of the poor.

The bravest people I have met are all Catholic priests. Working in West Papua and then in Brazil, I met men who were prepared repeatedly to risk death for the sake of others. When I first knocked on the door of the friary in Bacabal, in the Brazilian state of Maranhão, the priest who opened it thought I had been sent to kill him. That morning he had received the latest in a series of death threats from the local ranchers' union. Yet still he opened the door.

Inside the friary was a group of peasants – some crying and trembling – whose bodies were covered in bruises made by rifle butts, and whose wrists bore the marks of rope burns. They were among thousands of people the priests were trying to protect, as expansionist landlords – supported by police, local politicians and a corrupt judiciary – burned their houses, drove them off their land, and tortured or killed those who resisted.

I learned something of the fear in which the priests lived when I was beaten and nearly shot by the military police. But unlike them, I could move on. They stayed to defend people whose struggles to keep their land were often a matter of life or death: expulsion meant malnutrition, disease and murder in the slums or the goldmines.

The priests belonged to a movement that had swept across Latin America, after the publication of A Theology of Liberation by Gustavo Gutiérrez in 1971. Liberation theologists not only put themselves between the poor and the killers, they also mobilised their flocks to resist dispossession, learn their rights and see their struggle as part of a long history of resistance, beginning with the flight of the Israelites from Egypt.

By the time I joined them, in 1989, seven Brazilian priests had been murdered; many others across the continent had been arrested, tortured and killed; Óscar Romero, the archbishop of San Salvador, had been shot dead. But dictators, landlords, police and gunmen were not their only enemies. Seven years after I first worked in Bacabal, I returned and met the priest who had opened the door. He couldn't talk to me. He had been silenced, as part of the church's great purge of dissenting voices. The lions of God were led by donkeys. The peasants had lost their protection.

The assault began in 1984 with the publication by the Congregation for the Doctrine of the Faith (the body formerly known as the Inquisition) of a document written by the man who ran it: Joseph Ratzinger, who later became Pope Benedict. It denounced "the deviations, and risks of deviation" of liberation theology. He did not deny what he called "the seizure of the vast majority of the wealth by an oligarchy of owners … military dictators making a mockery of elementary human rights [and] the savage practices of some foreign capital interests" in Latin America. But he insisted that "it is from God alone that one can expect salvation and healing. God, and not man, has the power to change the situations of suffering."

The only solution he offered was that priests should seek to convert the dictators and hired killers to love their neighbours and exercise self-control: "It is only by making an appeal to the 'moral potential' of the person and to the constant need for interior conversion, that social change will be brought about." I'm sure the generals and their death squads were quaking in their boots.

But at least Ratzinger has the possible defence that, being cloistered in the Vatican, he had little notion of what he was destroying. During the inquisition in Rome of one of the leading liberationists, Father Leonardo Boff, Ratzinger was invited by the archbishop of São Paulo to see the situation of Brazil's poor for himself. He refused – then stripped the archbishop of much of his diocese. Ratzinger was wilfully ignorant. But the current pope does not possess even this excuse.

Pope Francis knew what poverty and oppression looked like: several times a year he celebrated mass in Buenos Aires's Villa 21-24 slum. Yet, as leader Argentina's Jesuits, he denounced liberation theology, and insisted that priests seeking to defend and mobilise the poor remove themselves from the slums, shutting down their political activity.

He now maintains that he "would like a church that is poor and is for the poor". But does this mean giving food to the poor, or does it mean also asking why they are poor? The dictatorships of Latin America waged a war against the poor, which continued in many places after those governments collapsed. Different factions of the Catholic church took opposing sides in this war. Whatever the stated intentions of those who attacked and suppressed liberation theology, in practical terms they were the allies of tyrants, land grabbers, debt slavers and death squads. For all his ostentatious humility, Pope Francis was on the wrong side.

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• A fully referenced version of this article can be found at Monbiot.com