Uganda's Minister for Ethics and Integrity Simon Lokodo plans to ban 38 pro-gay groups which he claims promote homosexuality.
The announcement follows police raids on gay rights workshops ordered by Lokodo.
'I have got a record of meetings that they have held to empower, enhance and recruit [homosexuals],' Mr Lokodo told Reuters.
Although the non-governmental organizations which he intends to 'de-register' have not been named yet, activists say if the plans go ahead it will not only effect LGBT campaign work in Uganda.
Award-winning activist Frank Mugisha, of Sexual Minorities Uganda (SMUG), said: 'NGOs in Uganda don’t just do LGBT work but also do work on HIV/AIDS, legal support for women and other things, so if they were shut down these groups it will effect lots of different groups of people in the country.'
Mugisha's Ice Breakers group opened Uganda's first ever LGBT sexual health clinic on 3 June, providing a 'life-line' for the country's persecuted gay community.
Mugisha added that the clinic is now under threat but added that he is optimistic that the government will not follow through with the ban.
'I wouldn’t have thought they would take such action and I’m still very optimistic that it is just political and they are just intimidating and scaring us,' he said.
'I don’t think they will go ahead with it. They might shut down some NGOs but I don’t think it will be all 38 in Uganda. However, there might be a problem for NGOs to renew their non-government operating licenses.'
Bisi Ailimi, who is Africa director of international LGBT charity Kaleidoscope, said any ban on gay NGOs would be a 'violation of fundamental human right'.
'This is an unnecessary reaction from the Ugandan government,' he told GSN.
He added: 'It is a shame that what is happening in Uganda contradicts what the Ugandan High Commission in London has been promising us – of fair play and protection for LGBT activists.
'LGBT organizations in Uganda such as SMUG and health clinics will be arrested, detained and charged for felony.'
Homosexuality is illegal in Uganda and Catholic bishops in Uganda called for a revival of the Anti-Homosexuality Bill, which proposes for the execution of gays in the African country.