Father Peter Donnelly, of Drumaroad parish, near Ballynahinch, Co Down, is under investigation over a complaint going back to the 1980s.
Fr Donnelly took up the ministry in Drumaroad three years ago and the Catholic Church has not disclosed where the alleged crime took place.
A spokesman from the diocese of Down and Connor stressed that the priest denies the claim.
"A complaint in relation to child safeguarding has been made against Fr Peter Donnelly, parish priest of Drumaroad," he said. "This complaint dates back to the 1980s.
"Fr Peter Donnelly denies this complaint. Fr Peter Donnelly, who has not been interviewed by the police as yet, will co-operate fully with the investigation.
"Fr Donnelly has voluntarily agreed to relinquish all pastoral duties while the investigation is being pursued. During the period of the investigation, Fr Donnelly continues to enjoy the natural right of every person to the presumption of innocence.
"In accordance with the paramountcy principle to safeguard children, the diocese of Down and Connor is co-operating fully with the civil authorities in their investigations in regard to this complaint. The diocese continues to work through its professional staff and its trained personnel together with the civil authorities in order to promote the safety of children."
He added: "I ask all of you to remember in your prayers all victims of sexual abuse and all who have suffered in any way because of that abuse. I ask you to keep Fr Peter Donnelly and all parishioners in your prayers at this time.
"We continue to encourage anyone who has a concern of a safeguarding nature to contact the PSNI, social services or the Diocesan Designated Safeguarding Officer."
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