The 13th century redundant church is a Grade 1 listed building under the care of the Churches Conservation Trust.
Its isolated location has meant that the building has suffered from criminal damage and graffiti in the past, and this most recent incident is thought to have occurred some time in June.
PCSO Billy Spence, of Mablethorpe Neighbourhood Policing Team, said: “This beautiful building has great architectural and historical importance and attracts visitors from across the UK.
“We should be very proud that we have such a gem in our area and it is extremely sad that someone would deface it in this manner.
“I would appeal to anyone who has information about those responsible to contact me on 101, quoting incident 239 of June 27”.