Slovakia's education minister, Milan Ftacnik, suspended the plans after discussions with leaders of the country's Roman Catholic and Lutheran churches, Bishops Frantisek Tondra and Julius Filo.
Government sources said at least 400 teachers had been trained by the Yoga in Daily Life society to introduce the Hatha Yoga system on a voluntary basis at gym sessions in primary and secondary schools.
But church leaders believed that the plans threatened Christian culture, according to Daniela Zemlova, international secretary of Slovakia's Lutheran church.
She said that the education minister, a yoga adept, had agreed to establish a commission with church participation to devise an alternative "relaxation program" for schools.
Yoga, which combines Hindu mystic and ascetic disciplines, teaches liberation of the self and union with the "supreme spirit," but is better known in Europe and the United States for its breathing and meditation exercises.
Hatha Yoga, which traces its origins to 12th century Indian philosophy, stresses mastery of the body as a way of attaining spiritual perfection.
A spokesperson for Slovakia's Roman Catholic Bishops' Conference, Marian Gavenda, said that independent experts had rejected the "methodological basis" of the scheme, which was designed by an Indian guru, Swami Maheshwarananda.
The bishops' conference had earlier issued a pastoral letter describing yoga as "a path to total atheism" and saying that Slovak Christians did not need to "search for some dubious substitute faith."
The plans had also led to friction within Slovakia's ...