Communications Minister Faith Muthambi has told members of the interim SABC board that they cannot proceed with their job until they have been vetted by the state security department.
Her letter to the board members on Wednesday comes less than a week after the board was appointed by President Jacob Zuma.
Muthambi said she would countersign Zuma's decision after security clearance had been granted.
She referred to a section of the Constitution that states that a written decision by the president "must be countersigned by another Cabinet member if that decision concerns a function assigned to that other Cabinet member".
A source with inside knowledge of the letter confirmed its contents.
Communications ministry spokesperson Mish Molokeng told News24 on Thursday that Muthambi was "simply bringing the vetting process to the attention of the new board members because it is an inherent and critical step in appointing members to the SABC board".
On Sunday Zuma, announced the appointment of Khanyisile Kweyama, John Matisonn, Mathatha Tsedu, Febe Potgieter-Gqubule and Krish Naidoo for six months.
Kweyama and Tsedu were appointed as chairperson and deputy chairperson of the SABC board respectively.
The notice was posted with the president's signature in the Government Gazette on Wednesday.
In the letter Muthambi asks the board members to send a copy of their identity books to her ministry to "facilitate security clearance as the South African Broadcasting Corporation is declared as a national key point in terms of the National Key Point Act".
She said the SABC board reported to Parliament via the executive authority for communications in terms of the Public Finance Management Act.
Thus, her signature was necessary, she said.
She asked them to declare any direct or indirect interests in line with section 16 and 17 of the Broadcasting Act.
"You are therefore required not to commence with your duties as an interim board member until the security clearance process has been conducted by the State Security Department."
Zuma made the appointments in terms of section 15A (3) of the Broadcasting Act (Act 4 of 1999), and on the recommendation of the National Assembly.
"Millions of South Africans rely on the public broadcaster for news, information and entertainment. We wish Ms Kweyama and her team well as they begin the important task of leading and revitalising one of the most important national resources, the SABC," said Zuma on Sunday.
The public broadcaster has not been able to function optimally due to several troubling issues
The previous management team was accused of unnecessary expenditure, corruption, censorship and other allegations that crippled the organisation.
The Auditor General's report last year disclosed irregular expenditure at the SABC.
Parliament's portfolio committee on communication on Thursday visited the SABC as part of its week-long oversight visit to various communication entities.
SABC spokesperson Kaizer Kganyago referred queries to Muthambi's office, saying he was in a meeting with the committee.
The committee chair Humphrey Maxegwana had not yet responded to a request for comment at the time of publishing.