A Catholic bishop in Spain is being investigated by the Vatican over an allegation of abuse that the cleric firmly denies, his diocese said in a statement on Monday.

Spanish paper El Pais first reported earlier on Monday that Bishop Rafael Zornoza was under investigation over an allegation of sexual abuse of a teenage boy in the 1990s.

According to the diocese's statement Zornoza is temporarily suspending his schedule while the case is investigated and will cooperate fully with the inquiry.

Zornoza, who has led the Diocese of Cadiz y Ceuta on Spain's southern coast since 2011, is the first Spanish Catholic bishop publicly known to have been investigated by the Vatican for an allegation of abuse.

For decades, the 1.4 billion-member Church has been shaken by scandals around the world involving abuse and cover-up, damaging its credibility and costing it hundreds of millions of dollars in settlements.

The Vatican press office did not immediately respond to a request for comment on the case.

The Cadiz y Ceuta diocese said the allegations were being investigated by a Church tribunal that was being convened at the Vatican's embassy to Spain, located in Madrid.

"The accusations being made, referring to events that took place nearly thirty years ago, are very serious and also false," said the diocese.

"There is full confidence in the justice system, and full cooperation will be provided in everything that is required," said the statement. 

"At the same time, it is necessary to remember to respect the presumption of innocence that applies to all persons."