Revd Patrick Sartie who works with the group Feed the Minds says many of the normal practices of a church service are having to be skipped.
He's concerned over the impact the disease is having on the relationships between people within churches.
He said: "We are no longer allowed to perform important church rituals and people are not allowed to show love in church in the same way.
"Handshaking is a sign of love and it is part of the custom of my church. When people started avoiding handshake for fear of the Ebola virus, some people became offended with their friends and families."
He says he's been banned from serving communion, sharing the peace, burying and marrying church members.
"The church is somewhere where people should come together, not be kept apart." he said.
Feed the Minds has had to suspend much of its work through its literacy and education projects in Sierra Leone.
It's working to support Revd Sartie so that the correct information about Ebola is given to people who need it and ensuring everyone is literate about the disease.