Jorge Bergoglio was head of the Jesuit order in the 1970s when the church backed military government and called for patriotism

Despite the joyful celebrations outside the Municipal Cathedral in Buenos Aires yesterday, the news of Latin America’s first pope was clouded by lingering concerns about the role of the church – and its new head – during Argentina’s brutal military dictatorship.

ADVERTISEMENT

The Catholic church and Pope Francis have been accused of a complicit silence and worse during the “dirty war” of murders and abductions carried out by the junta that ruled Argentina from 1976 to 1983.

The evidence is sketchy and contested. Documents have been destroyed and many of those who were victims or perpetrators have died in the years that followed. The moral argument is clear, but the reality of life at that time put many people in a grey position. It was dangerous at that time to speak out and risk being labelled a subversive. But many, including priests and bishops, did so and subsequently disappeared. Those who stayed silent have subsequently had to live with their consciences — and sometimes the risk of a trial.

Its behaviour during that dark period in Argentine history was so unsaintly that in 2000 the Argentine Catholic church itself made a public apology for its failure to take a stand against the generals. “We want to confess before God everything we have done badly,” Argentina’s Episcopal Conference said at that time.

In February, a court noted during the sentencing of three former military men to life imprisonment for the killings of two priests that the church hierarchy had “closed its eyes” to the killing of progressive priests.

As head of the Jesuit order from 1973 to 1979, Jorge Bergoglio – as the new pope was known until yesterday – was a member of the hierarachy during the period when the wider Catholic church backed the military government and called for their followers to be patriotic.

ADVERTISEMENT

Bergoglio twice refused to testify in court about his role as head of the Jesuit order. When he eventually appeared in front of a judge in 2010, he was accused by lawyers of being evasive.

The main charge against Bergoglio involves the kidnapping of two Jesuit priests, Orland Yorio and Francisco Jalics, who were taken by Navy officers in May 1976 and held under inhumane conditions for the missionary work they conducted in the country’s slums, a politically risky activity at the time.

His chief accuser is journalist Horacio Verbitsky, the author of a book on the church called “El Silencio” (“The Silence”), which claims that Bergoglio withdrew his order’s protection from the two priests, effectively giving the military a green light for their abduction.

ADVERTISEMENT

The claims are based on conversations with Jalics, who was released after his ordeal and later moved to a German monastery.

Bergoglio has called the allegations “slander” and holds that, on the contrary, he moved behind the scenes to save the lives of the two priests and others that he secretly hid from the death squads. In one case, he claims he even gave his identity papers to one dissident who looked like him so that he could flee the country.

ADVERTISEMENT

For some, that makes him a hero. Other are skeptical. Eduardo de la Serna, co-ordinator of a left-wing group of priests who focus on the plight of the poor, told Radio del Plate that: “Bergoglio is a man of power and he knows how position himself among powerful people. I still have many doubts about his role regarding the Jesuits who went missing under the dictatorship.”

Many in the church are keen to move on from that dark period in the history of Argentina and the church. They say the new pope helped to heal the wounds of the dirty war and to restore the credibility of the Catholic hierarchy.

“As archbishop, he faced a monumental task, and he was even accused of collaboration with the dirty war, which he strenuously denied and was ultimately cleared. If he can restore the credibility of the church there [in Argentina], he can handle the scandals that have befallen the church worldwide because he knows how to connect to the people” said Ramon Luzarraga, theologian-in-residence at the University of Dayton.

ADVERTISEMENT

But the issue is unlikely to go away any time soon, particularly while high-profile trials are still taking place. This week a Buenos Aires court sentenced the “Last Dictator” Reynaldo Bignone to life in jail for crimes relating to the disappearance of 23 people, including two pregnant women, when he was in power in the 1980s.

guardian.co.uk © Guardian News and Media 2013