Eric de Moulins-Beaufort, head of the Bishops' Conference of France, said that secrets shared in the confessional are above the law.
France's top bishop has been summoned by the interior minister after saying that the pact of secrecy would prevent a priest from reporting sex crimes against children that were revealed during Catholic confession.
Following the publication of a report this week about sexual abuse of children by the clergy, Eric de Moulins-Beaufort, who is archbishop of Reims and head of the Bishops' Conference of France, said in a radio interview that the secrecy of the confession rite takes precedence over the laws of the republic.
Under French law, anyone who is aware of a sex crime against a minor is obliged to report it to the authorities and risks heavy fines and imprisonment if failing to do so.
"Nothing takes precedence over the laws of the republic in our country," French government spokesman Gabriel Attal said on Thursday.
He added that Interior Minister Gerald Darmanin - who also oversees religious issues - would receive de Moulins-Beaufort next week at the request of President Emmanuel Macron "in order to make sure that things are clear".
In the Catholic religion, confession is a rite during which sinners acknowledge their sins to a priest and seek forgiveness from God. It is usually performed anonymously in a confession booth, behind a screen, so that the priest can hear but not see the penitent.
"Confession must remain secret because it opens a space where one can speak freely... before God," de Moulins-Beaufort said on franceinfo radio.
De Moulins-Beaufort said it was unlikely that many pedophiles would admit to their crimes during confession and that even if they did, it would be in euphemistic terms.
He added that when children indicate during confession that they are being abused, the church must look for other ways to help them speak out. "Many children only speak during confession because they know it is secret," he said.