Malan also dismissed allegations that the former National Party government had established a "sinister and shadowy third force" to target its opponents.
Testifying before a special Truth and Reconciliation Commission hearing in Cape Town, Malan also told of his involvement in South Africa's chemical and biological warfare programme and of orders he gave for cross-border raids against "enemy targets" in southern Africa.
Malan volunteered to testify at the public hearing on the role of the SADF during the apartheid years at a recent meeting with TRC chairman Archbishop Desmond Tutu, who chaired Wednesday's hearing.
Among the members of the public listening to his testimony were retired army generals Jannie Geldenhuys, Kat Liebenberg and Constand Viljoen and former NP cabinet ministers Andre Fourie and Abe Williams.
Malan opened his two-hour long submission by taking political and moral responsibility for the actions of SADF members during the 1970s, when he was defence force chief, and later as defence minister under President PW Botha.
The SADF had never considered itself to be above the law. Soldiers who transgressed the law were court-martialled, Malan said.
The former NP government had missed a "golden opportunity" to create a climate of reconciliation when it failed to legislate a general amnesty before the 1994 general election, he said.
"If the former government had fulfilled its responsibility in respect of a general amnesty, to which the ANC was inclined in those days, this Truth and Reconciliation Commission... would have been unnecessary."
He was closely questioned by TRC national investigations head Glenn Goosen on a top-secret document recommending the "elimination" of five Renamo members suspected of killing Renamo secretary-general Orlando Christina in April 1983.
Christina was living on a farm owned by the SADF just outside Pretoria at the time of his death.
Goosen put it to Malan, who was then defence minister, that Orlando's death would have been embarrassing to the SADF as South Africa's support for Renamo had not been officially confirmed by the government.
He said one of the five men identified for elimination, Bonaventura Bomba, had been killed. The fate of the other four was not known.
Goosen said the document, which he handed to Malan, had been written by a working group comprising the police investigating officer, a military intelligence officer, Capt PJ Viljoen and Commandant Wouter Basson of the SA Medical Services, who later headed South Africa's chemical and biological warfare programme.
Goosen said the group had recommended the murders of the five.
Malan said he had no recollection of the document and would not have approved the murders.
"It was reported to me that he (Christina) had been killed by fellow Renamos and that it was being investigated. They said they were handing the matter over to Renamo to sort out."
In confirming his role in setting up the CCB as a component of SADF special forces, Malan said the unit had provided the defence force with good covert capabilities.
"The role envisaged for the CCB was the infiltration and penetration of the enemy, the gathering of information and the disruption of the enemy."
He said it had been set up with 10 divisions or regions, eight of which referred to geographical areas. One of these, region six, referred to South Africa.
However, he had only learnt in November 1989 that region six had been activated and the unit had begun to operate in South Africa.
"The police came foward and said elements of the CCB were operating in Johannesburg. I queried it. They (the CCB) said they had a regional element. I was surprised.
"At that stage I thought it was the exclusive responsibility of the police to operate in South Africa and not the SADF."
He said his approval had not been necessary to activate the unit.
As a professional soldier and later as minister of defence he had issued orders which led to the death of innocent civillians in crossfire.
"However, I never issued an order or authorised an order for the assassination of anybody, nor was I every approached for such authorisation by any member of the SADF."
The killing of political opponents of the government, such as the murder of University of the Witwatersrand academic Dr David Webster had never been SADF policy.
Malan said he had authorised the establishment of South Africa's chemical and biological warfare programme, codenamed Project Coast, in 1981 to counter chemicals being used by Cuban and Soviet forces in Angola.
"This project did not have sinister connotiations. At no time did I authorise the use of any chemicals developed by Project Coast."
As defence minister he had also authorised "numerous" cross-border raids against enemy targets in southern Africa.
"These raids caused bloodshed. As a Christian I regretted the loss of lives but unfortuntately that is the reality of war."
He said he would not apply for amnesty for these operations as he considered them legal actions of the state.
He also told the TRC panel that it should accept the "stark reality" that the former government had never established a covert "third force" to target opponents.
He said the now-defunct State Security Council had investigated the possibility, in 1986, of establishing a special counter insurgency and unrest police police unit as a third force.
However, the recommendation had been rejected in favour of expanding the police's counter-insurgency ability.