A statue of St Anthony's at the shrine in Pallakandal, Puttalam was vandalised on Tuesday.
The church falls under Chilaw parish.
The vandalism comes amid heightened security at churches across the island following the Easter Sunday suicide bombings which targetting luxury hotels and churches, leaving over 250 people dead.
The iconic St Anthony's church in Colombo was one of the churches targetted by bombers, alongside the Zion church in Batticaloa and St Sebastian's church in Negombo.