In an interview with the Catholic daily yesterday, the pope said it would be "contradictory, imprudent" to seek Cardinal Philippe Barbarin's resignation at this stage.
"We will see after the end of (any) trial. But (to seek his resignation) now would be to imply guilt," the pontiff said.
Francis said he believed Barbarin had "taken the necessary measures, he took things in hand. He is brave, creative, a missionary. We should now wait for the outcome of the civilian judicial procedure."
Preynat was placed under formal investigation in January, but his lawyer argues the alleged crimes are now beyond the statute of limitations.
In March, prosecutors in Lyon ordered a preliminary investigation into three accusations by civilian plaintiffs that Barbarin's diocese knew about the scandal a number of years ago but failed to inform the authorities.
According to the diocese, Barbarin first received testimony from an alleged victim in mid-2014, and relieved Preynat of priestly office in May 2015.
One of the group's founders, Francois Devaux, told AFP that the pope did not have enough information to be able to exclude Barbarin's resignation.
"He is lacking many of the elements needed to have a clear idea of the situation. I think the pope does not have all the ins and outs (of the situation) to consider that Cardinal Barbarin should remain in place," Devaux said.
The Lyon diocese has not made an official comment on the report. A source close to the cardinal however said the pope was commenting for the first time on the matter and that it was "an expression of confidence between two men who know and respect each other.
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