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.