Fire caused extensive damage to Church of Loaves and Fishes, where perpetrators left Hebrew graffiti denouncing the worship of idols.
Israel police and the Shin Bet arrested three Jewish youth who are suspected of being involved in the arson at the Church of Loaves and Fishes in northern Israel about a month ago.
Immediately after the incident the police arrested 16 youths, all yeshiva students from West Bank settlements, but released them shortly after.
A covert investigation led the Shin Bet to the three suspects.
In an initial investigation by the fire brigade there were indications that the fire broke out in several places in the affected compound pointing to the fact that arson had been committed.
The church, which Christians believe is where Jesus performed the Miracle of the Multiplication of the Loaves and the Fishes, lies on the shores of the Sea of Galilee and is a traditional site of pilgrimage in the Holy Land.