Instructor Cori Withell said the classes she booked for yoga and pilates at St Edmund's Church building in Southampton were cancelled with 10 days to go.
She was told by the booking secretary of the church that it was because yoga is a Hindu religious activity.
Father John Chandler from the church said that the hall has to be used for Catholic activities and he banned it because it was advertised as ''spiritual yoga''.
The ban is not Catholic Church policy and decisions are left to the discretion of individual priests. Some Catholic retreats use yoga for relaxation.
Ms Withell, 37, from nearby Eastleigh, said the church accepted the booking two months ago and she paid £180.
She was called later and told that yoga was from another religion so she could not have the hall. A separate pilates class she had booked was also cancelled.
''I had never heard about any religious issue with yoga before but I have looked into it since and found that some other religions feel that when people meditate it could let the devil inside them,'' she said.
''But there was never any meditation in my class - it was just exercises. Yoga is not religious: spiritual, but not religious.
''I do not object to anyone having a religious viewpoint, but it seemed terribly petty to cancel the classes.
''As a nation we have an obesity epidemic. I was trying to bring some exercise to the community and coming across blocks like this is frustrating.
''I offered to go down and show them the moves and, literally, the shutters came down.''
Fr Chandler said the church was ''misled'' by Ms Withell's booking because he claimed that, at first, the hall was booked for pilates and then he found out it was also for spiritual yoga.
''Yoga is a Hindu spiritual exercise. Being a Catholic church we have to promote the gospel and that's what we use our premises for.
''We did say that yoga could not take place. It's the fact that it's a different religious practice going on in a Catholic church,'' he explained.
''On one hand we say to our parishioners 'be strong in your faith', and on the other hand there's this other religious belief that's not part of our faith. It's not compatible. We are not saying that yoga is bad or wrong.''
Fr Chandler added he had not researched what Ms Withell's class would have included and he had not spoken to her about the issue because he felt ''the relationship had got off to a bad start''.
''There are other halls she could use in Southampton,'' he added.
A spokesman for Portsmouth Catholic Diocese said: ''It's not possible for Catholic premises to be used for non-Christian activities and there is a dilemma with yoga as it can be seen as Hindu meditation or as relaxation.
''There is no national policy on this and the decision is for each priest.''