The group said the government’s move to make the Coalition of Malaysia NGOs (Comango) illegal was a “disturbing assault on freedom of expression”.
The Home Ministry on Wednesday said some of the 54 groups in Comango were not registered with the government.
It also said some of Comango’s objectives, including promoting gay rights, were against Islam.
Mohamad Khalid Shariff, the ministry’s secretary-general, said in a statement that Comango was representing “rights that run contrary to Islam”. This included the interests of gay, lesbian and trans-gender people, he said.
He added that only 15 of the 54 Comango organisations were registered under a 1966 government act that allowed groups to operate in the country.
Comango also represents other marginalised groups, including women, children, Christians and immigrant workers, in the Muslim-majority nation, says the BBC’s Jennifer Pak in Kuala Lumpur.
Amnesty International’s Malaysia arm is part of Comango.
“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, a Malaysia researcher at the group, said in a statement.
Comango last year angered the government with a report it gave to the United Nations condemning the country’s human rights record ahead of a review.
Malaysia’s ruling coalition, in power for 57 years, has faced criticism over its human rights record and freedom of religion.
While it retained power in the most recent elections, the result was the coalition’s worst ever.