JOHANNESBURG — SERIOUS fault lines stemming from the apartheid era are coming into sharper focus as the new government grapples with a security apparatus and state bureaucracy long geared toward perpetuating white rule and undermining anti-apartheid resistance.
President Nelson Mandela - who is visiting the United States this week to address the United Nations, meet President Clinton, and promote foreign investment among business leaders - has set national unity and reconciliation at the top of his political agenda.
But the continued presence in the police force of senior officers identified with the apartheid oppression is fueling a growing perception among the rank-and-file of the African National Congress that the ANC leadership has not taken sufficient action to eradicate the old order.
In order to get a firm grip on the levers of power, Mr. Mandela must break through a wall of resistance from vested interests in the state bureaucracy and security apparatus, while keeping day-to-day government flowing.
Nowhere is that task more difficult than in regard to the so-called third force, covert elements in the apartheid-era security forces and state bureau- cracy that have continued to exist after the transition to democracy.
Some leading figures in the ``third force'' in the military have been flushed out. But there are still scores of senior officers in the police force who were either actively involved in a campaign of assassination and terror against apartheid foes or had full knowledge of such activities.
In-depth interviews with Mandela, Deputy President Frederik de Klerk, right-wing Freedom Front leader Gen. Constand Viljoen, and figures in the security establishment who prefer to remain anonymous have led to the conclusion that the legacy of the third force is unresolved.
This third force, they say, continues to exploit violence between rival taxi groups in the black townships and the violent political conflict in KwaZulu/Natal Province between Zulu supporters of the ANC and the Inkatha Freedom Party (IFP).
Tensions are mounting in the new government of national unity over how to deal with the past and flush out third-force elements. The major areas that will test Pretoria's unity include:
* Establishing the form, powers, and mandate of a truth and reconciliation commission - whose task will be to grant indemnity from prosecution to perpetrators of past political crimes in return for disclosure, identify human rights violations, and make reparations to apartheid victims.
* Flushing out remaining elements in the security forces - particularly the South African Police Services - who were instrumental in delaying the democratic transition through political violence.
* Restructuring a white-dominated bureaucracy without disrupting government, redefining national interests, and bringing the intelligence community in line with the new order.
Though long suspected to exist, the first conclusive evidence of a third force came with a surprise raid on a military intelligence front company in October 1992 by Judge Richard Goldstone's commission on political violence, revealing clandestine efforts to discredit the ANC.
SADF Chief of Staff Pierre Steyn, working under Judge Goldstone's commission, conducted an investigation that ultimately led to then-President De Klerk suspending 23 senior South African Defense Force officers.
In April - shortly before the elections - Goldstone lifted the lid on a third force operating within the police force by exposing a gun-running racket to Chief Mangosuthu Buthelezi's IFP with top-level police involvement.
DEPUTY Police Commissioner Basie Smit has gone on early retirement; Military Intelligence Chief of Staff Gen. Christoffel van der Westhuizen - the man regarded as the ringleader of third-force elements in the SADF - has taken early retirement; and Col. Eugene de Kok, the suspected head of an elaborate third-force network in the police, was indicted in August on 13 criminal charges, including murder and attempted murder.
But civil rights workers feel that to make a clean break with the past, it is necessary to expose other leading third-force figures and to establish how the chain of command operated - who was acting under orders and who exceeded their mandates.
There is growing concern in political and diplomatic circles that the proposed truth commission will fail to achieve these objectives if it starts a witch hunt.
De Klerk, who was named head of the key Cabinet committee on security and intelligence under Mandela's oversight last week, told the Monitor he still had major problems with the latest draft legislation setting up the truth commission. His concerns relate to the lack of con-fidentiality of disclosure by those seeking indemnity from prosecution, vagueness of the mandate regarding former political crimes by ANC members, and the meth-od of selecting commissioners.
The task of flushing out the third force will increasingly lie with the new national intelligence structures that combine former rival ANC and government security agencies. This will mean sanitizing and downgrading the old Department of Military Intelligence and the old Security Police, both of which orchestrated the campaign to defeat the anti-apartheid resistance.
``The new government has started to work out what was going on in the security forces in the final stand of the apartheid regime, but they have discovered a minefield and don't quite know what to do about it,'' says a former intelligence officer now researching the third force. ``The problem is they are not listening to the people who really knew how the old system worked.''