The mother of the alleged victim filed a case for sexual assault on her son in the 1990s against a priest in Bayonne on Wednesday and he has been relieved of his functions.
In a letter published on the diocese's website Bayonne Archbishop Marc Aillet said he had notified the legal authorities of the case on 15 April and promised to cooperate with the investigation.
The priest has already tried to commit suicide twice - once after being investigated for allegedly molesting his nephew on a camp in Poland, the other time during a scandal over the molesting of a teenage girl in 2007.
He went into therapy after that attempt and on arriving in the diocese Archbishop Aillet met him and assigned him to tasks that did not involve contact with children, according to his letter.
Former monk admits sex abuse in France and Côte d'Ivoire
On Friday Régis Peillon, formerly Brother Jean-François Régis, is to appear in a court in Chalon-sur-Saône, Burgundy, after admitting two cases of sexual abuse, one against a teenager in 2009, the other against a fellow monk five years later, both in France.
Peillon belonged to the Saint Jean monastic community, whose leaders knew about several cases he had been involved him but failed to notify the authorities, according to the Mediapart investigative website.
Régis was "exfiltrated" from Côte d'Ivoire in 2008 after abusing several teenagers and young adults while in charge of a hostel there, the site claims.
A spokesman for the community told the AFP news agency that he had been asked to hand himself over to the police over the Côte d'Ivoire cases and that brought the French cases to light.
Two other former Saint-Jean monks have been convicted of sexual assault by French courts and another committed suicide before going to trial in 2012.
The Vatican has ordered an inquiry into the community, founded in 1975.
One of its founders, Father Marie-Dominique Philippe, preached a doctrine of "friendship love", which victims' group Avref claims could be used to justify "any type of physical relationship regardless of the age or sex of the prospective partner".
Lyon bishop accused of cover-up
Earlier this month the church summoned France's bishops to a conference on paedophilia in the wake of a series of scandals, notably an investigation into whether Lyon Archbishop Philippe Barbarin covered up at least six cases of sexual abuse in the diocese.
Two other legal complaints have been filed - one in French Guiana, the other near Orleans - since the Lyon scandals hit the headlines.