"Yoga is forbidden for Muslims. The practice will erode their faith in the religion," Abdul Shukor Husin, chairman of the government-backed National Fatwa Council, told reporters.
"We advice Muslims not to practice yoga. It does not conform with Islam," he said in response to a call to ban Muslims from doing yoga
Islam is the official religion of Malaysia, where more than 60 percent of the population of 27 million are Muslim Malays who practice a conservative brand of the religion.
Yoga, an ancient Indian aid to meditation dating back thousands of years, is a popular stress-buster in Kuala Lumpur.
Zakaria Stapa, a professor at the Islamic faculty of the National University of Malaysia, recently called on Muslims to stop doing yoga as it could cause them to "deviate from their faith".
Abdul Shukor said yoga involved physical and religious elements of Hinduism including the recitation of mantras.
He could not say how many Muslims were practising yoga but called on state authorities to punish those who do.
The fatwa council, one of Malaysia's highest Islamic bodies, recently banned women from dressing or behaving like men and engaging in lesbian sex, saying it was forbidden by the religion.