Pope Francis is sending the Catholic Church's top sexual abuse investigator to Chile to look into accusations a bishop covered up crimes against children, just days after the pope defended him.

A Vatican statement said new information had emerged about Bishop Juan Barros and that the investigator, Archbishop Charles Scicluna of Malta, would go to "listen to those who want to submit information in their possession".

The statement, which gave no further details, was a U-turn for the pope, who last week told reporters aboard his plane returning from Latin America he was sure Archbishop Barros was innocent and that the Vatican had received no concrete evidence against him.

It was Archbishop Scicluna who uncovered evidence of sexual abuse that led to the removal of the late Mexican priest Marcial Maciel, founder of the Legionaries of Christ, in 2005.

Controversy over Archbishop Barros, bishop of the city of Osorno in Chile's south, dominated Francis' recent trip, with critics accusing the pope of not understanding the depth of the crisis in the South American country.

Archbishop Juan Barros

A number of men have accused Archbishop Barros of protecting his former mentor, the Reverand Fernando Karadima, who was found guilty in a Vatican investigation in 2011 of abusing them and others when they were boys.

Karadima always denied the allegations, and Archbishop Barros said he was unaware of any wrongdoing.

During the trip to Latin AMerica, a Chilean reporter managed to get close to the pope at an event and shouted out a question about Archbishop Barros.

"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.

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His comments were widely criticised by victims, their advocates and newspaper editorials in Chile and the pope's native Argentina.

Even Cardinal Sean O'Malley of Boston, a key papal adviser on how to root out sexual abuse in the church, distanced himself with a statement saying the pope had caused "great pain".

Speaking to reporters on the plane returning to Rome, Francis apologised to victims, acknowledging that his choice of words and tone of voice had "wounded many".

Victims and their advocates have said Francis should never have appointed Archbishop Barros because there had been accusations against him.

Anti-Barros parishioners demonstrated during his investiture ceremony in 2015.

"We were surprised by the Pope's decision, because we spent three years trying to reach him to put an end to this issue," said Juan Carlos Claret, a spokesman for Osorno parishioners.

"This shows that the pope is responding more to the pressure from the media than he is to the faithful."

While the pope, who met two victims in Chile during the trip, has vowed "zero tolerance" of sexual abuse, a planned Vatican tribunal to judge bishops accused of covering up abuse or mishandling cases has not started.

The much-touted commission Cardinal O'Malley heads has been hit by defections by high-profile non-clerical members who quit in frustration over what they said was lack of progress.