The culprits entered the premises of the Holy Hill Church in the wee hours of yesterday and damaged the altar, flower plots and other belongings, police said.
Police Commissioner Seemanth Kumar Singh along with other police officials inspected the spot. A case has been registered.
Condemning the attack, Deputy Speaker of Karnataka Assembly Yogish Bhat said police had been asked to trace the culprits and initiate strict action against them.
"I cannot tolerate attacks and defiling of places of worship including churches in my constituency," he said.
Senior Congress leader Janardhan Poojary accused the Sangh Parivar behind the attack on the church. It was deliberate and pre-planned, aimed at vitiating communal harmony in the region.
He urged the police to launch proper investigation immediately.