Correctional Services spokesman Manelisi Wolela has denied allegations that student leader Mcebo Dla.
Acting President Kgalema Motlanthe yesterday announced his new cabinet which included many of those who had resigned earlier in the week.
Speaker Baleka Mbete was elected deputy president of the Republic.
The DA's parliamentary leader Sandra Botha welcomed Mbete's appointment because "I have absolute faith in her".
Motlanthe made wholesale changes to the departments of health and defence, appointing new ministers and deputy ministers to these portfolios.
Minister of Health Manto Tshabala-Msimang was one of the ministers who did not resign, yet she was removed from her portfolio.
She was replaced by ANC MP Barbara Hogan.
Aids Law Project attorney Fatima Hassan said the ALP was "ecstatic about the appointment of Barbara Hogan".
"Manto Tshabala-Msimang should have been replaced a long time ago. Hogan is not a denialist," said Hassan.
Tshabalala-Msimang is now Minister in the Presidency, replacing Essop Pahad, who also resigned on Tuesday.
Molefi Sefularo became the deputy minister of health, filling the vacancy left by Nozizwe Madlala-Routledge who was fired by former president Thabo Mbeki last year.
Charles Nqakula was also removed from his post as Minister of Safety and Security and replaced by ANC Chief Whip Nathi Mthethwa.
Nqakula will now be the Minister of Defence, replacing Mosioua Lekota, who resigned on Tuesday.
Nqakula's deputy is Fezile Bhengu, who replaced deputy defence minister Mluleki George.
Geraldine Fraser-Moleketi, Minister of Public Service and Administration, also resigned on Tuesday and was replaced by ANC MP Richard Baloyi.
Intelligence Minister Ronnie Kasrils, who said he would not be coming back after he resigned on Tuesday, was replaced by Siyabonga Cwele.
Sicelo Shiceka becomes Minister of Provincial and Local Government, replacing Sydney Mufamadi who also resigned on Tuesday.
MP Geoff Doidge becomes Minister of Public Works, replacing Thoko Didiza who resigned on Tuesday.
Former Public Enterprises Minister Alec Erwin, who said he would not be available for re-appointment, was replaced by Justice Minister Brigitte Mabandla. Mohamed Surti becomes the new Justice Minister.
Trevor Manuel, who resigned on Tuesday, was re-appointed as Minister of Finance.
Unpopular Minister of Correctional Services Ngconde Balfour, who is currently embroiled in allegations of corruption over his alleged links with Bosasa, a company charged with catering at a number of the country's prisons, was re-appointed Minister of Correctional Services.
Motlanthe said he was "in discussions with Azapo that its leader Mosibudi Mangena should continue as Science and Technology Minister".
Thabo Mbeki's long-time friend Aziz Pahad, who also resigned on Tuesday, was re-appointed Deputy Minister of Foreign Affairs.
Nkosazana Dlamini-Zuma, Nosiviwe Mapisa-Nqakula, Lindiwe Sisulu, Ivy Matsepe-Casaburri, Zola Skweyiya, Membathisi Mdladlana, Jeff Radebe, Naledi Pandor, Buyelwa Sonjica, Lindiwe Hendricks, Makhenkhesi Stofile, Marthinus van Schalkwyk, Mandisi Mpahlwa, Pallo Jordan, and Lulu Xingwana all kept their cabinet posts.