Unlike whites, who were relatively prosperous and had access to developed infrastructure, blacks continued to live in underdeveloped conditions and only had a theoretical right to equal opportunity.
The longer this situation persisted, the more entrenched would be the conviction that the concept of nation building was a mere mirage, Mbeki said in a special debate on national reconciliation.
However, abolishing the apartheid legacy would require considerable effort over a considerable period of time.
Referring to German unity, he said the seriousness with which the German people treated their process of promoting national unity and reconciliation was reflected, among other things, by the extraordinary volume of resources which the richer, developed West Germany, transferred to the poorer and relatively, underdeveloped East.
During the first five years of unification after 1990, US586,5 billion of public funds were transferred from West to East Germany to underwrite German national unity and reconciliation.
South Africa's own "solidarity tax" was imposed for one year only, accompanied by much grumbling from some sectors of society, he said.
Mbeki said the various political parties and society at large were not behaving in a manner which promoted reconciliation and nation building.
"Are the relatively rich, who, as a result of an apartheid definition, are white, prepared to help underwrite the upliftment of the poor, who... are black?"
The South African Revenue Service (SARS) was engaged in a difficult struggle to ensure that every individual and corporate entity met their tax obligations, he said.
The SARS had established that about 30 percent of corporations were not registered for tax.
"These are people who, by honouring their legal obligations, could make an important contribution to addressing the material challenges of national unity and reconciliation.
"They deliberately choose not to, but will not hesitate to proclaim that the goverment has failed to `deliver'," Mbeki said.
On affirmative action, he said that in the majority of cases the call for transformation of the public and private sector had been resisted with great determination.
"To ensure that it does not happen, some of what is said is that `black advancement equals a white brain drain' and `black management in the public service equals inefficiency, corruption and a lowering of standards'."
By ignoring that South Africa's past determined the present, "it comes about that those who were responsible for or were beneficiaries of the past, absolve themselves from any obligation to help do away with an unacceptable legacy", Mbeki said.
The current situation suggested that the Truth and Reconciliation Commission would be unable to compete its work, especially with regard to the full disclosure and attribution of many acts of gross human rights violations.
"This will leave the law enforcement agencies with no choice but to investigate all outstanding cases of such violations, making it inevitable that our society continues to be subject to tensions which derive from the conflicts of the past."
Some South Africans, including those within the security forces, were prepared to go to any length to oppose the democratic order, including the assassination of leaders and destabilisation by any means, Mbeki said.
These included the now well-known story of former freedom fighters allegedly wishing to overthrow the government, as well as other disinformation campaigns which the intelligence services were investigating.
These also involved allegations that Safety and Security Minister Sydney Mufamadi was involved in the cash-in-transit robberies, while he (Mbeki) and Deputy Defence Minister Ronnie Kasrils were responsible for the murder of white farmers.
However, the overwhelming majority of South Africans had not abandoned the goal of national unity and reconcilation, nor lost hope that it would be realised, he said.
There were significant numbers of people, including those among the white and Afrikaner community, who were demonstrating a real commitment to ensuring unity and reconcilation became a reality, Mbeki said.