Argentinian human rights activists have raised questions about the activities of the new pope more than 30 years ago, during the country's so-called dirty war.
In the 1970s and 80s the military junta kidnapped and killed thousands of people in order to eliminate leftist opponents.
The Vatican denies reports that at the time Jorge Mario Bergoglio, now Pope Francis I, refused to protect two Jesuit priests who were subsequently kidnapped and tortured.
In 2000 the Argentinian Catholic church apologised for its failure to take a stand against the junta, which held power between 1976 and 1983.
In 2005 a human rights lawyer filed a criminal complaint against him, accusing him of unspecified involvement in the kidnapping of two priests.
After years of rumours, the future Pope told his biographer he in fact made secret interventions to save the men's lives.
The Vatican says the allegations are defamatory and there has never been any accusation that is concrete or credible.
A papal spokesperson has described the accusations as old "slander", which Australia's top Catholic, Cardinal George Pell, agrees with.
"Those stories have been dismissed years and years ago," he told the ABC.
"There was a telephone call, the head of Amnesty International at the time said those charges were completely false.
"They were a smear and a lie and they've been laid to rest years ago."
Cardinal Pell, the Archbishop of Sydney, and one of the men who took part in the conclave to elect the new Pope, said the allegations had not been considered during the conclave's deliberations, reports the ABC.