Chelsea Brears of Quesnel, a small town in British Columbia, objected to the breathing and stretching exercises used at her son's school.
The yoga techniques have been adopted by schools participating in the Action Schools keep-fit scheme, a programme launched two years ago after it emerged that a quarter of the province's children were overweight or obese.
In one part of the sessions, students would kneel, put their hands together above their heads in the shape of a candle and repeat the word "Namaste" - an Indian expression used in greeting or parting - which translates roughly as "I bow to you".
Mrs Brears protested, telling the Canadian Broadcasting Corporation: "It's not fair to take prayer (out of the schools), and yet they're allowing yoga, which is religion."
She was supported by Audrey Cummings, a local rancher, who told the Vancouver Province: "If you're not seeking the God of the Bible, then by default you're in the other camp."
The parents' concerns are not entirely baseless - historically, yoga was one of six schools of Hindu philosophy. But, as school officials pointed out, the keep-fit exercises used in the West have little or nothing to do with Hinduism.
Nonetheless, schools have bowed to pressure and replaced yoga with skipping, dancing and calisthenics.