Prime Minister Abdullah Badawi has bowed to pressure from conservative Muslims, shutting down a series of forums on religious freedom.
The order is directed at Article 11, a coalition of 13 Muslim and non-Muslim human rights NGOs named after the article in the constitution that guarantees freedom of religion.
Mr Abdullah, who has urged debate and religious tolerance, announced the decision late on Tuesday after chairing a high-level meeting of the ruling United Malays National Organisation.
'Article 11 forums must stop immediately because they are deemed to cause tension in our multi-religious society,' Mr Abdullah said.
The move is a reversal of his policy to promote transparency and open discussion.
Article 11 argues that all citizens have the freedom of worship or not if they chose, but conservative Muslims see it as a threat which invests Muslims with the secular right to abandon their religion.
On Sunday, about 10,000 Muslims, led by prominent lawyers and politicians, protested against Article 11 at a mosque in the capital, demanding that Mr Abdullah end the debate.
That rally followed another last week which saw about 2,000 Muslims protest outside a forum in Johore state and the storming and breaking up of an Article 11 forum in Penang in June.
Muslims are also angry with Article 11 for backing Lina Joy, a Muslim convert to Christianity, who has applied to the court to drop the word 'Islam' from her national identity card.
Prominent Muslim conservative leader Mahfuz Omar said Muslims welcomed Mr Abdullah's decision to end the debate.
'No citizens should question Islam's pre-eminent position in Malaysia,' he said.
Rights activists, however, remained adamant the debate on religious freedom should continue.
'We cannot sacrifice the right to free expression,' said Article 11 member Yap Swee Seng, executive director of Suaram, a leading human rights organisation. 'The clash between the dual Islamic and secular systems of law must be addressed by proper debate and not swept under the carpet. The problem will only surface later.'
Ivy Josiah, head of the Article 11 secretariat, said no more forums would be held but the group was seeking to meet Mr Abdullah.
'There is a lot of misconception about Article 11. We are not against Islam, nor are we promoting apostasy,' she said. 'We are merely restating the obvious that all citizens must respect Article 11.'