Cardinal Seán Brady, archbishop of Armagh and Primate of All Ireland, sent his condolences to Archbishop Julián Barrio Barrio, on behalf of all the Irish bishops.
Nearly 80 people were killed and another 130 injured.
The wreck Wednesday is still under investigation, though initial reports say the train was traveling at a velocity as much as double the speed limit set for the curve in the tracks where it derailed.
Spain declared three days of mourning.
"We are offering prayers for those who have died, those who have been injured, and their families," Cardinal Brady wrote. "The entire Catholic community here in Ireland is spiritually close to you and all who have been affected at this time and I assure you of our on-going prayers.
"I pray through the intercession of Saint James, Apostle, that those who have been injured will be speedily restored to full health."