In its final report released in Pretoria, the TRC said the National Intelligence Agency was still systematically demolishing documents about two years ago.
"Culpability lies with the officials directly responsible, but the agency's top management must be held accountable," the TRC document said.
The commission said the former cabinet in 1993 officially sanctioned the mass destruction of state documents, which already started in 1990.
"The intention was to deny a new government access to apartheid secrets through a systematic purging of official memory.
"The former government deliberately and systematically destroyed a huge body of state records and documentation in an attempt to remove incriminating evidence and thereby sanitise the history of oppressive rule."
The TRC said apartheid-era bodies who took part in this mass destruction included the security branch of the police, the National Intelligence Service, intelligence services of the former homelands governments, the State Security Council, the SA Defence Force, Military Intelligence, the Department of Prison Services and the Department of Justice.
The report stated that the former State Archives Service should be held accountable for indecisive and ineffective steps it took to halt "the destruction endeavour".
"While there is evidence that SAS attempted to secure a degree of professional autonomy, it is highly improbable that apartheid imperatives did not mould selection decisions."
Head of the Security Secretariat Johan Mostert should also be held accountable, because he had sent a circular to all government departments in July 1993 recommending the destruction of classified documents.
The TRC said liberation movements failed to exercise all the leverage at their disposal to stop the destruction.
The loss of documents had a severe impact on South Africa's social memory, the commission said.