The 53-year-old priest and his 57-year-old assistant were allegedly digging a hole inside the 150-year-old church in the district of Kilkis, north of Thessaloniki, hoping to find hidden archaeological treasures.
Locals reportedly tipped off the police late on Thursday after hearing loud noise coming from the church. Police discovered a two-meter deep, one-meter wide tunnel behind the altar, and confiscated sacks full of earth, digging tools and two pairs of gloves.
Another four people are being charged in connection with the illegal dig, a police statement said.
Hundreds of churches were burgled last year and faced with a rapid rise in the number of break-ins over the past few years, forcing priests across the country to take more measures to protect church property.