Silver Street Baptist Church and St James's Anglican Church in Taunton, Somerset have turned away Louise Woodcock's Yum Yum Yoga class for toddlers.
Woodcock defended her classes, saying that they had no religious content at all, and only involved music and movement.
She said: "I explained to the church that my yoga is a completely nonreligious activity. Some types of adult yoga are based on Hindu and Buddhist meditation but it's not a part of the religion and there is no dogma involved.
"This is a class for mums and children, which has yoga-inspired moves - but as soon as I mentioned the word yoga the church staff completely changed their attitude. They have completely misunderstood and are being narrow minded."
Originally the Baptist Church did grant Yum Yum Yoga use of its hall for a children's group activity, The Times has reported, however, Rev Simon Farrar withdrew his consent after discovering it was for yoga.
Woodcock then went to St James's Church but was rejected for the same reason.
Rev Farrar explained the decision: "We are a Christian organisation and when we let rooms to people we want them to understand that they must be fully in line with our Christian ethos.
"Clearly, yoga impinges on the spiritual life of people in a way which we as Christians don't believe is the same as our ethos.
"If it was just a group of children singing nursery rhymes, there wouldn't be a problem but she's called it yoga and therefore there is a dividing line we're not prepared to cross."
The Rev Tim Jones, vicar of St James's, supported the decision, saying: "Any alternative philosophies or beliefs are offering a sham - and at St James's Church we want people to have the real thing. Yoga has its roots in Hinduism, and attempts to use exercises and relaxation techniques to put a person into a calm frame of mind - in touch with some kind of impersonal spiritual reality.
"The philosophy of yoga cannot be separated from the practice of it, and any teacher of yoga, even to toddlers, must subscribe to the philosophy.
"Yoga may appear harmless or even beneficial, but it is encouraging people to think that there is a way to wholeness of body and mind through human techniques - whereas the only true way to wholeness is by faith in God through Jesus Christ."