It is five years since Pope Benedict XVI stunned the Roman Catholic world by announcing he would resign. His time in office had been blighted by the emergence of terrible stories of sex abuse and institutional cover-up. Even though most of these dated from the time of his predecessors, Benedict’s efforts to make things right were clumsy and inadequate to the scale of the problem. His successor, Pope Francis, seemed as if he were going to change all that as part of the openness, energy and realism that has characterised his approach. But developments in recent weeks have cast Francis’s sincerity and seriousness into question and threaten to overshadow many of the other accomplishments of his papacy.

Earlier in his pontificate, Francis had to deal with the enforced departure of one of his closer collaborators, Cardinal George Pell, who left the Vatican to face charges of historic child abuse, which he vigorously denies, in his native Australia. Several members of the church’s commission for the protection of minors, which the pope had set up, resigned in protest at the obstructionism of some parts of the Vatican bureaucracy; but these are the parts that are thought hostile to Francis, too, so he was not widely blamed for what happened.

All that changed with the pope’s visit to Chile. The church there had been convulsed by the discovery that children had been abused by an influential priest for years. It is claimed that many other priests knew or even witnessed what was going on. Among them was Juan Barros, whom Francis made a bishop in 2015 and installed in a southern diocese in the teeth of furious protests from both clergy and congregation. Bishop Barros, who denies the claims, was prominent among the bishops who received Francis on his visit: the two men were photographed embracing; and when Francis was asked on the flight back what he thought of the allegations against the bishop, he replied that they were merely slander, and that he had not seen any proof to back them up.

This was outrageous enough. He later apologised for his language, saying it must have come as “a slap in the face” for survivors. He has sent the Vatican’s chief prosecutor to Chile to reinvestigate the case. But he reiterated his belief in Bishop Barros’s innocence. Now it emerges that an eight-page letter detailing the accusations against the bishop was handed to the pope by Cardinal Sean O’Malley, the man in charge of relations with survivors, who is trusted by both sides.

Either the pope failed to read the letter or he read and then discounted it. Either explanation must damage his reputation, and he has legions of enemies inside the church who want to destroy him. Most of these enemies denounce him for appealing to lay people over the heads of the priesthood, especially when it comes to sexual morality. In the case of Bishop Barros he seems to be committing a dreadful mistake by siding with the clergy and the establishment over the instincts of his flock.