"A small stone of the size of 1-2 centimetres was thrown at the St Joseph Vaz worship centre near Deralakatte, damaging the windowpane, but no damage has been done to the idols of Mother Mary and Infant Jesus," Mangaluru City Police Commissioner S Murugan said.
Karnataka Health minister U T Khader visited the spot.
Murugan said the incident could have been carried out by a mischief-monger, but it could not be established immediately whether a group of people were involved.
"We are probing the matter. For now, we only know that only one stone has been pelted. We are finding out whether there was an individual or group behind the stone
A case had been registered and investigations were on.
The incident might have occurred late Tuesday night or in the early hours of Wednesday, Murugan said.
Breaking his silence on a spate of church attacks, Prime Minister Narendra Modi had recently said his government will not allow any religious group to incite hatred and will strongly act against any religious violence.
The prime minister, who has been accused by opposition and Christian groups of turning a blind eye to a string of recent attacks on five churches and a Christian school in Delhi, had said his government "gives equal respect to all religions".
Assistant Commissioner of Police Shankar Shetty, who visited the spot, told media persons that the culprits had not been identified.
The incident would be taken seriously in the wake of the series of church attacks in Delhi, he said.
Budget 2015: Bollywood expects FM to streamline taxes
Markets riding for a fall unless budget delivers
Plea for CBI inquiry into AIIMS graft: HC seeks Centre's reply
Friction over India's beef trade heats up after attacks