Malaysia's Home Ministry issued a statement on Wednesday 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.
Amnesty, whose Malaysian arm is under COMANGO, denounced the move.
"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.
It remains unclear how the ministry's ban will affect COMANGO activities or those of its members.
AFP