Malaysia's Home Ministry issued a statement yesterday declaring the Coalition of Malaysian NGOs (COMANGO) illegal because the group and 39 of its 54 components were not registered with the government.
Ministry secretary-general Mohamad Khalid Shariff accused COMANGO of pursuing "rights that run contrary to Islam" including gay, lesbian and transgender issues.
The coalition angered authorities last year when it submitted a report to the United Nations condemning the Muslim-majority nation's human rights record ahead of a UN rights review.
"Outlawing COMANGO is a deeply disturbing action aimed at silencing important critical voices that have advocated on the world stage for Malaysia to uphold international human rights law and standards," Hazel Galang-Folli, Malaysia researcher at Amnesty International, said in a statement.
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It remains unclear how the ministry's ban will affect COMANGO activities or those of its members.
Malaysia's 57-year-old ruling coalition, which guided the country's transition to a regional economic success, has long applied a firm hand to rights groups and other critics.
Authorities have used arrests and court charges to apply pressure.
But the opposition and other critics have labelled that pledge a cynical vote grab, alleging continued curbs on democratic freedoms.
The ruling coalition retained power in May but with its worst showing ever and since then the political situation has been tense.
The opposition has repeatedly staged protests challenging the outcome, while the government has responded by levelling sedition charges at some of its most vocal opponents.