Cardinal Sean O'Malley, the archbishop of Boston, said he could not explain why Francis "chose the particular words he used".
In an extraordinary effort at damage control, Cardinal O'Malley insisted that Francis "fully recognises the egregious failures of the church and its clergy who abused children and the devastating impact those crimes have had on survivors and their loved ones".
Francis sparked national uproar upon leaving Chile on Thursday by accusing victims of the country's most notorious paedophile priest of having slandered another bishop, Juan Barros.
The victims say Bishop Barros knew about the abuse but did nothing to stop it - a charge which the bishop denies.
"The day they bring me proof against Bishop Barros, I'll speak," Francis told Chilean journalists in the northern city of Iquique.
"There is not one shred of proof against him. It's all calumny. Is that clear?"
The remarks shocked Chileans, drew immediate rebuke from victims and their advocates and once again raised questions over the 81-year-old Argentine Jesuit's stance on the issue.
The scandal over the crimes of the Rev Fernando Karadima has devastated the credibility of the Roman Catholic Church in Chile, and Francis' comments will likely haunt it for the foreseeable future.
Cardinal O'Malley's carefully-worded critique was remarkable since it is rare for a cardinal to publicly rebuke the Pope in such terms.
But Francis' remarks were so potentially toxic to the Vatican's efforts to turn the tide on decades of clerical sex abuse and cover-up that he clearly felt he had to respond.
Cardinal O'Malley headed Francis' much-touted committee for the protection of minors until it lapsed last month after its initial three-year mandate expired. Francis has not named new members, and the committee's future remains unclear.
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