“I apologise to them if I hurt them without realising it, but it was a wound that I inflicted without meaning to,” he said. “It pains me very much.”

Last Thursday, a Chilean reporter managed to get close the pope at the end of an event and shouted out a question about Barros, of the diocese of Osorno, who is accused of protecting a notorious paedophile.

“The day I see proof against Bishop Barros, then I will talk. There is not a single piece of evidence against him. It is all slander. Is that clear?” the pope replied in a snippy tone.

His comments were seen as trying to dismiss the credibility of accusers and was widely criticised by victims, their advocates and newspaper editorials in Chile and the pope’s native Argentina.

Francis said on the plane: “I know how much [abuse victims] suffer in hearing the pope say to them ‘bring me a letter with the proof,’ I realise that it is a slap in their faces, and now I realise that my expression was an unfortunate one”.

Barros has been accused of protecting his former mentor, the Rev. Fernando Karadima, who was found guilty in a Vatican investigation in 2011 of abusing teenage boys over many years. Karadima denies the allegations, and Barros said he was unaware of any wrongdoing.

Barros was among the men Karadima trained about 20 years ago. Barros and three others went on to become bishops. A Chilean, Juan Carlos Cruz, said Barros saw Karadima abuse him.

In his comments on the plane, the pope disclosed that Barros had offered to resign twice in recent years but Francis rejected the offers.

“I can’t condemn him because I don’t have evidence and because I am convinced he is innocent,” Francis said.

He said Barros would remain in his place unless credible evidence is found against him.

On Saturday, even Cardinal Sean O‘Malley of Boston, a key papal adviser, distanced himself with a statement saying the pope had caused “great pain”.

That statement was even more remarkable because O‘Malley heads a papal commission advising the pontiff on how to root out sexual abuse in the Church.

While on the plane with journalists, Pope Francis also said that he had come under fire for previously marrying a couple on a plane during his South American tour.

“Someone told me I was crazy to do something like that,” he joked.

In the first such ceremony on a papal flight, Francis married Paula Podest Ruiz, 39, and Carlos Ciuffardi Elorriga, 41, both cabin attendants on Latam airlines.

While the gesture made world headlines and was mostly well-received by Catholics, conservative Catholic commentators and bloggers who regularly criticise the pope on a host of issues blasted the wedding at 36,000 feet.

They said it would make it difficult for pastors to deal with Catholic couples who want to get married in unusual secular locations instead of a church. Those couples would say “the pope did it, why can’t you?” one commentator wrote.

But the pope said the situation of the Chilean couple was a particular one because they had been already been married in a civil service eight years ago and were not able to marry in their parish church because it collapsed in a 2010 earthquake.

“I questioned them [about marriage] and the responses were clear … it was clear they had made a commitment for life,” the pope said, adding that the couple had even remembered subjects from the Catholic pre-marriage courses they had taken long ago.

“Tell the pastors that they were prepared and I made a judgment call. The sacraments are for people. All the conditions were clear,” he said.