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.

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.