Major non-governmental organisations that have taken the government to court on behalf of ordinary citizens are teetering on the brink of financial collapse after being deregistered or found to be non-compliant.
Equal Education, the NGO that successfully sued the Basic Education Department last year, and the Treatment Action Campaign, which forced Thabo Mbeki's government to provide antiretrovirals to pregnant HIV-positive women, are two of thousands of organisations affected.
Once deregistered or found to be non-compliant, NGOs are unable to access government or lottery money.
Last year, 85000 NGOs were registered in South Africa.
According to the Department of Social Development website, only 28280 organisations are currently registered.
Figures from the Non-Profit Organisation Directorate, which monitors the sector for the department, show that just over 36488 organisations have been deregistered and are no longer valid NGOs. Some 35204 were listed as non-compliant.
Charities Aid Foundation CEO Colleen du Toit said it had been inundated in recent days with requests from NGOs needing help to register again.
Du Toit questioned whether the government was attempting to crack down on the non-profit sector. She described the moves to deregister or list as non-complaint more than two-thirds of all NGOs in South Africa as "sinister".
As a result of the mass deregistrations, large donors wanted to cease funding NGOs.
Du Toit said: "One of our largest corporate clients checked their list of beneficiaries and all of them have been deregistered. These are all reputable organisations with long-standing reputations and excellent relationships with donors.
"Imagine if all corporates think the same - given that they provide at least 25% of the funding of the NPO sector."
Du Toit said: "The de-registrations are unconstitutional and in contradiction of the NPO Act.
The Act stipulated "the department had to notify organisations in writing before deregistration or marking of non-compliance. This was not done."
The problem has been exacerbated by the disbandment of the appeal panel before which NGOs can argue to be registered again.
Former appeals panel member Ann Bown said this made it difficult for the more than 30000 deregistered NGOs to appeal the decision or get reasons for being deregistered.
The Endangered Wildlife Trust, an environmental group that has been in South Africa for 40 years and is active in fighting rhino poachers, found out only yesterday that it had been deregistered.
CEO Yolan Friedmann said the Social Development Department had not contacted the trust once in 12 years.
The trust was audited and posted its financial statements and annual reports on its website. It provided donors with additional information on request.
Other well-known NGOs deregistered include the Legal Resources Centre, which is helping to represent miners at the Marikana commission of inquiry.
The centre was involved in court cases last year that forced the Department of Education to hire and pay temporary teachers in the Eastern Cape and fill thousands of vacant posts.
Equal Education secretary Doron Isaacs said declaring thousands of NGOs non-compliant was extreme and the department was in breach of administrative law.
Department spokesman Lumka Oliphant said only about 29000 of 108600 NPOs on the department's system were fully compliant with the requirements of the NPO Act.
"The auditor-general has been dissatisfied for the past six years with the department's non-monitoring of the NGOs. It has been his view that the department does not know where the money given to the organisations goes."