Very few Argentines were on hand for the proceedings, for the white smoke followed by the traditional proclamation, Habemus papam “We have a pope.”

But on the other side of the world, the people of Buenos Aires erupted with jubilation when they learned that the new pontiff, Pope Francis, was Argentine.

The celebration was more about national pride than religious pride, however. At the moment that Cardinal Jorge Mario Bergoglio has become the face of Catholicism in the Southern Hemisphere and the world, his own country is becoming far less religious.

Only about 25 percent of Argentines regularly attend church far below the 44 percent attendance rate in the United States and evangelical Protestantism is growing in popularity.

Even churchgoing Catholics in Argentina, like their counterparts in North America, flout the church’s dictates about marriage, birth control and education.

Perhaps that explains why, so soon after the celebrations, a dark and sobering question came to the fore: What did Pope Francis do during the “dirty war”?

Bergoglio, 76, was about to turn 40 when the Argentine military seized power from President Isabel Peron in March 1976.

A military junta, led by Gen. Jorge Rafael Videla, opened a shock campaign, claiming it was necessary in order to rid the country of communists.

The man who is now pope was the leader of the Jesuit order in Argentina during that dark period of the 1970s and 1980s. He was there when Videla and his band of generals turned a battle against a small group of leftist subversives into a murderous campaign against teachers, doctors, unionists, intellectuals, Jews and, sometimes, activist priests.

When it was over, an estimated 10,000 to 30,000 people had “disappeared” and were presumed dead.

For survivors and the families of the disappeared, questions remain as to how much was done or could have been done to stop the violence. Some have said that strong pressure on the military leaders many of whom were as ardently Roman Catholic as they were anti-communist might have tempered their actions.

These survivors say that neither the Argentine Catholic Church nor the Vatican, or many individual priests, raised their voices to protest the slaughter of innocents.

Then-Cardinal Bergoglio defended himself against charges that he failed to speak out in his 2010 autobiography “El Jesuita” (“The Jesuit”). “I did what I could do at my age at the time, and with the few contacts I could count on, to advocate on behalf of people who had been kidnapped,” he wrote.

The controversial Argentine journalist Horacio Verbitsky has claimed that Bergoglio failed to protect two former Jesuits at the height of the violence. The two activist priests had been seized shortly after Bergoglio expelled them from the Jesuit order.

Adolfo Perez Esquivel, the Argentine human rights activist and pacifist who won the Nobel Peace Prize in 1980, defends the new pope.

Though Perez Esquivel acknowledged Thursday that some members of the Catholic clergy were complicit with the military junta indeed some torture survivors testified that priests were present during torture sessions Perez Esquivel said Bergoglio was no friend of the military junta and should not be blamed.

As for Bergoglio’s efforts to help detainees such as the two Jesuits named by Verbitsky, Perez Esquivel said in an interview with BBC World that even when priests and bishops such as Bergoglio “petitioned the military junta for the liberation of prisoners and priests, they didn’t grant their requests.”

Cardinal Bergoglio’s elevation to the papacy has revealed once again the depth and complexity of Argentina’s memories and attempt to deal with the repression of that period.

The Catholic Church is still defending its role during World War II, and its sins of omission and commission vis-a-vis Adolf Hitler and anti-Semitism, almost three-quarters of a century later.

It seems certain that Pope Francis, too, will have to grapple with claims and counterclaims that he should have done more in the face of external evil. But if nothing else, the church’s less than perfect record may help it deal with its imperfections now, especially as Francis confronts a moral crisis within the church itself.

• Peter Eisner, Los Angeles Times