The suspect, aged 63, allegedly committed the acts when he was alone with the children at the parish church of Santa Rosa de Santa Coloma de Gramenet in Barcelona during bible study classes in December and January.
The eldest brother reported what had happened to his parents on January 29th and subsequent investigations revealed that his two younger siblings had also suffered abuse, according to Catalan police.
La Voz De Galicia newspaper reported that the priest, known as I.M, had allegedly perpetrated the offences when he was alone with the boys, so each remained unaware of what had happened to the others.
The priest appeared in court on Thursday, charged with sexual abuse.
Police have not ruled out the possibility that other boys may also have been molested.
The office of the Archbishop of Barcelona stated that although the priest had been relieved "of all parish functions and responsibilities." they "respected the presumption of innocence," and that the action was a precautionary measure.
The arrest occurred on the same day that the United Nations called publicly on the Vatican to "immediately remove all known and suspected child sexual abusers from assignment and refer the matter to the relevant law enforcement authorities for investigation and prosecution purposes."
The UN Committee on the Rights of the Child said that the Catholic Church was still failing to do enough to live up to its stated commitment to stamp out child abuse by priests and lay employees.
It underlined its "deepest concern about child sexual abuse committed by members of the Catholic churches who operate under the authority of the Holy See, with clerics having been involved in the sexual abuse of tens of thousands of children worldwide."
Fittingly in light of the events in Barcelona it noted: "Dozens of child sexual offenders are reported to be still in contact with children."