The warning came in a meeting between Environment Minister Richard Benyon and a Church of England delegation that included representatives of Natural England.
Mr Benyon was told that bat conservation was damaging churches not only physically but financially.
Second Church Estates Commission and leader of the delegation, Sir Tony Baldry, told of how the cost of replacing a small piece of leaded window had jumped from £5 using plain glass to £140 in order to fit the lead 'bat flap' required by the Bat Conservation Trust.
The cost is equivalent to four weeks' collection in the rural parish church of Wiggenhall, St Germans.
Concerns were also raised about the health and safety impact of bats, and their role in the spread of disease.
The Venerable Paul Ferguson, Archdeacon of Cleveland, said the congregation of St Hilda's Ellerburn had so far spent £29,000 addressing two bat problems.
"Although a licence to do something is now promised, it is by no means certain. Meanwhile, the cost in financial and human terms to those who worship there continues," he said.
The delegation reminded the minister that churches were places of worship, heritage sites and community centres, and not sites of special scientific interest.
They expressed support for measures that would mitigate the impact of bats on buildings.
The Bishop of Norwich, the Right Reverend Graham James said: "I remain puzzled as to why our churches are treated as if they were uninhabited barns. They are not."
The Church of England has been working on the issue with DEFRA and Natural England but Chair of the Church Buildings Council, Anne Sloman, said she was "deeply depressed" by the lack of progress.
"The minister was clearly sympathetic but the challenge is to convert sympathy into action," she said.
"There has been over-delegation to the Bat Conservation Trust (BCT) which approaches the issue as a bat welfare group and not the impartial scientific organisation that should be giving advice on how to interpret the law."
Sir Tony said: "We need action now. Many of my colleagues in the House of Commons are as frustrated as I am by the lack of progress. I'm sure they feel, as I do, that we can't go on, year after year, saying something will be done when it isn't."