They have even removed human remains from the disused space near All Saints Church in Loughborough, forcing it to perform special prayers so they can be reinterred.
All Saints Church was built in the 14th Century however it was constructed on grounds which already housed graves - meaning the badgers could be digging up remains well over 700 years old.
Bodies are no longer buried in the churchyard but parishioners regularly walk through the area.
The Church has informed Charnwood Borough Council which manages the land. They've put an application into Natural England who're expected to provide a licence by the end of November to allow them to close down the badger setts.
Speaking on Premier's News Hour Rev Wendy Dalrymple said: "Well it is on my long list of things that they don't teach you at vicar school.
"Some people are obviously a little bit upset. We're not used to seeing bones in our daily life so sometimes people feel a bit: 'oh gosh, has there been a murder?"
"Some present me with a bone and I say 'yes, thank you very much' and then bring it into church.
"It would be lovely if they weren't here because quite frankly I've got other things to do with my time."
Listen to Premier's Antony Bushfield speaking to Rev Wendy Dalrymple on the News Hour:
