The Islamic authorities have issued a ruling, known as a fatwa, instructing the country's Muslims to avoid yoga because of its Hindu roots.
To most people yoga is simply a sport - a stress-busting start to the day.
Malaysia's National Fatwa Council said it goes further than that and that elements of the Indian religion are inherent in yoga.
Announcing the decision, the council chairman Abdul Shukor Husin said practices like chanting and what he called worshipping were inappropriate and they could "destroy the faith of a Muslim".
The ruling is not legally binding but many of Malaysia's Muslims abide by fatwas.
Yoga classes here are filled with mostly non-Muslim Malaysians of Chinese or Indian descent, but in the major cities it is not uncommon to see several Muslim women at classes.
Prayers and gym
For Muslims across Malaysia the day starts at 5.30 in the morning, as the call to prayer goes out.
A handful of the most devout arrive at a mosque in the western outskirts of Kuala Lumpur.
Each is carrying a yoga mat, slung over their shoulder.
Adam Junid is a Muslim Malaysian who does both - prayers and gym, specifically yoga.
An engineer in his 30s, he goes to a weekly class for about 30 people.
"I don't think it interferes with the religion at all," he says.
"In fact it helps you, makes you healthy and more aligned and it helps you become self aware," he adds.
Adam is a rarity because it is mostly women and not many Muslims who do this.
Yoga comes in many forms. For some it is a stress-busting sport. For others a serious bit of soul searching.
What Adam does once a week is the serious stuff. The class I sat in on was two hours long.
It included breathing exercises, with the help of the tick-tock of a metronome.
There was meditation, then half an hour of darkness for intense relaxation.
Before that some of the class managed a very stable headstand. Others could touch the back of their head with their foot.
"It can go with any religion," instructor Mani Sekaran told me.
"Or it can go with those who don't believe in any religion, because it's purely sports," he added.
He is also founder of the Malaysian Yoga Society. A bald and very fit man, he once did martial arts.
"If I want to train for an Olympic gold medal... whether I believe in a religion or not doesn't matter. I just keep on training."
During the class I sat in on, yoga's Hindu roots were mentioned, albeit briefly. A spiritual experience was on offer for those who wanted it.
This is the point where some Muslims in Malaysia worry about yoga. They think it is encroaching on their way of life.
One Muslim student told me that she combined yoga techniques with prayers. That concerns some Islamic experts.
"If people want to practice yoga, the physical exercise, I think that is no problem," Professor Osman Bakar, from Malaysia's Institute of Advanced Islamic Studies, told me.
"Many Muslims would say fine. But they would object to the mixing of the two things."
"Islam is a complete way of life. Islam is able to cater to the needs of Muslims; spiritual needs, intellectual needs and other needs, material needs. So there is no need to bring in elements from outside," he added.
Adam's yoga class ended with a quick discussion about self-awareness, concentration and why people do yoga. I was not sure if this was a weekly occurrence or for my benefit.
He told me that yoga has made him a better person. He has no plans to stop.