The decision was taken after a number of problems arose between church-goers and beggars, reported Spanish newspaper El Diario.
The move was triggered by an incident at the Church of Our Lady of Carmen (Iglesia Nuestra Señora del Carmen) in the Indautxu neighbourhood of Bilbao.
In a statement released online, church authorities said: "Last Sunday we had to suspend 9am mass due to the disruptive presence of a man who was talking and shouting in a loud voice in the middle of the mass."
According to church authorities, the man had stolen several bags as well as the Christmas charity collection and was pestering people as they entered and left the church.
The statement described how church authorities had "reached their limit" with the disruptive behaviour of beggars around the city’s churches.
"We cannot encourage beggars", the church said, "most of them still young, who do not want to improve their situation."
The church added that if people did want to give money, they should donate to institutions such as the Catholic charity Cáritas "which distributes the money and helps people who want to get out of this deplorable situation".
This is not the first confrontation between the church and beggars in the Basque region in recent times. In November 2014 a beggar surprised the bishop of San Sebastián by bending down as if to kiss his ring, then stealing it from his finger.