He told a special meeting of the Truth and Reconciliation Commission in Cape Town that state terrorism and covert operations by the apartheid government and security forces did not end with the unbanning of the ANC and other organisations in 1990 and the start of negotiations.
"The consequences of these campaigns against the democratic opposition were far worse than anything experienced in the (state of) emergency years."
Between 1990 and 1993, nearly 12000 civilians were killed and 20,000 injured in many incidents, including several major massacres, Mbeki said.
The Human Rights Commission recorded the accelerating pace of assassinations of anti-apartheid figures; 28 in 1990, 60 in 1991 and 97 in 1992.
Mbeki said that a top secret document dated March 13, 1990 stated that De Klerk "was briefed on a broad spectrum of sensitive projects" and had given his approval "in principle" on the running of covert "Stratkom" projects.
The document also stated that "these projects were controlled and managed by the secretary of the SSC (the State Security Council)" who received decisions and orders regarding covert operations "from the State President and passes them on to the departments concerned".
The ANC said in its written submission that in 1990 the government changed the name of its centralised security structure, the National Security Management System to the National Co-ordinating Mechanism.
There had been attempts to propagate the idea that De Klerk had abolished the NSMS, that it was stripped of its security and intelligence components, "and became no more than an essential and benign co-ordinate structure".
"This is untrue," the ANC said relying on extracts from the NCM official handbook.
The NCM remained the old NSMS, and the security committees chaired by SAP or SADF officers from local to national level remained in place.
"As the official NCM manual notes: `The principle of the application of the full powers of the state in order to resist the revolutionary onslaught is still valid'," Mbeki told the commission.
There had been partial, yet telling revelations of the nature and extent of covert operations in the post-1990 phase, including the admission by Orde Boerevolk members after their escape to the United Kingdom that they were military intelligence agents with a specific brief to destabilise black communities and the ANC.
Other examples included the November 1992 Goldstone Commission raid on Pan Afrik Industrial Investment Consultants, a Directorate: Covert Collection front company, which provided glimpses of other operations, such as those aimed at subverting self-defence units, Mbeki said.
In its 100-page submission the ANC also sought to show government subversion of SDUs.
It said that when the government went on a full-scale offensive communities began to take steps to defend themselves by establishing defence committees, people's militia or self-defence units.
The ANC had actively encouraged this.
On August 6, 1990 the ANC formally committed itself to a cessation of armed hostilities, but between late August and late September, over 700 civilians had been massacred in attacks on homes, train commuters, and gatherings such as funeral vigils, Mbeki said.
Resolutions at an ANC consultative conference in 1990 committed the organisation to assisting people in setting up accountable and non-partisan SDUs, he said.
"It was, however, made clear that the overall control of SDUs was to remain with community structures and the MK cadres were to participate as members of the community."
However, the State had infiltrated and subverted SDUs to prevent communities from defending themselves, Mbeki said.
This was the case in the notorious Phola Park SDU, headed by a police informer who overthrew the popularly-recognised resistance committee and conducted a reign of terror in the area.