Christopher Chope, who is himself a former Environment Minister, told George Eustice that MPs were concerned that European legislation that oversees the flying mammals and called for the UK to take care of the issue.
Mr Chope suggested the regulations protecting bats should not apply to churches, in order to protect the historic buildings.
Speaking in the Commons, Mr Chope said: "It's a great concern to me, and I know to a lot of my honourable friends, that here we've got European legislation dealing with bats who don't fly across Europe.
"These are bats that reside in the United Kingdom, in the British Isles, and so what business is it of the other countries in the European Union to dictate to us how we should look after our own bat population?
"It seems to me in accordance with that much-vaunted but totally-ignored principle of subsidiarity that this almost would be a starting point - that the European Union would say if you've got a species in your country which is not moving from one country to another then it should surely be for the domestic law to deal with that rather than for European law.
"So, I'd be very interested to know from (Mr Eustice) where he thinks we've got to on that."
Mr Chope later withdrew his Bat Habitats Regulation (No. 2) Bill following reassurances from the minister about ongoing work to address his concerns.
In recent years the Church of England has seen increased numbers of bats using church buildings as roosts.
Last year Caroline Spelman MP, the Church of England's representative in Parliament, revealed the Church was working with the Department for Communities and Local Government regarding "changing the regulations" on bat roosts.