General Magnus Malan: Feared and notorious politician who waged a dirty war against the enemies of apartheid

The death of Magnus Malan marks the passing of one of the most powerful and notorious leaders of the apartheid era. To his enemies, he was a figure of fear and hatred – one of the monsters of an evil system; to his colleagues and subordinates he was a figure of awe – the general who reorganised the military and then reorganised the country along military lines.

Malan was the son of a biochemistry professor who went on to become an MP and Speaker of the House. The boy was despatched to a militarised academy and this forged his ambitions. After a year at university he defied his father's advice and signed up for the Permanent Force.

His rapid rise, which included a year's training at an officer's course in the US, led to his promotion as Chief of the army in 1973 and Chief of the Defence Force three years later. During this spell, the military was transformed, becoming a far larger, more efficient and more aggressive – particularly after PW Botha became Prime Minister in 1978.

The irascible Botha appointed the more avuncular Malan to his cabinet as Defence Minister and they became a double act that few dared challenge. They insisted the country was facing a "Total Onslaught", requiring a "Total Strategy" in response. This involved a relaxation of petty apartheid, combined with ever-more systematic and brutal crackdowns on opponents at home, and regular raids into neighbouring states. Frequently using verbs like "annihilate", "eliminate" and "exterminate", Malan even approved a programme of biological warfare, and under his watch, South Africa, assisted by Israel, became a nuclear power.

Malan's military also helped set up, arm and fund the Renamo terrorists in Mozambique and, together with the US, Unita in Angola. This came to an end in 1988 when the SADF failed to take the town of Cuito Cuanavale in Angola, which prompted their retreat and a series of setbacks at the hands of the Cubans, who were advancing towards the Namibian border. Malan played a key role in the subsequent negotiations that led to South Africa's withdrawal from its Namibian colony (and Cuba's from Angola).

Within South Africa, however, mass-based protests, consumer boycotts and other forms of opposition escalated, prompting the military to assume roles previously taken by the police. Malan, whose special talent was for macro-management, spearheaded the creation of the National Security Management System, which brought policing, intelligence and civic affairs under the sway of the generals. It was headed by the State Security Council, which set up the Civil Cooperation Bureau (CCB) – a death-squad network whose task was to assassinate opponents at home and abroad.

Like thousands of others, I had personal reasons to keep an eye on Malan. In 1989 the Harms Commission of Inquiry found that I was one of the CCB's intended assassination victims. They botched the job, but succeeded in murdering a close friend of mine, Dr David Webster. It later emerged that the decisions to kill David and I were taken by the State Security Council, on which Malan had a prominent seat.

As it happened, in this period I would regularly sit alongside this bald, bulky, jug-eared figure in a very different capacity: at boxing matches. Malan would plant himself in the press seats as a guest of the promoters, exuding a strong whiff of power and entitlement despite his bluff, good-old-boy bonhomie. By then, his long spell in a corruption-mired government had given him a taste for the high life, and the low. The first item on the agenda of many cabinet meetings was the list of sequestrated farms to be divided up among the faithful.

Malan and another cabinet minister, John Wiley, developed a friendship with an opportunistic businessman, Dave Allen, and together they used military helicopters and equipment to go on fishing trips to Bird Island near Port Elizabeth. In 1987 Allencommitted suicide after beingarrested for paedophilia, followed, soon after, by Wiley.

When investigating this story nearly a decade later I discovered that two mixed race boys had been sexually assaulted during one of these Bird Island expeditions. I eventually caught up with Malan, who, rather to my surprise, admitted knowing at the time that his friend was an alleged paedophile. "Yes, I heard," he said, adding enigmatically. "I heard a lot of things in my position."

Whatever his involvements, Malan was considered untouchable in the 1980s, but to retain that positionhe and his forces resorted to ever more brutal methods. As the "unrest" escalated, so did the military's reach.In 1984, they occupied black townships and began to fund, organise andtrain black proxy forces – in particular, Chief Mangosuthu Buthelezi's Inkatha movement. It is estimatedthat close to 20,000 people died in political violence during the 1980s and early 1990s, many as a result of military intervention.

Malan's demise coincided with Botha's. The old patriarch suffered a stroke in 1989 and was succeeded by FW de Klerk, who was far less beholden to the military. The general had a brief spell as Minister of Water Affairs and Forestries before bowing out.

He was charged with commissioning a massacre of 13 people (including seven children) in Kwa Makhutain 1987, but was acquitted. It was found that although Inkatha had been paid by the state to carry out the massacre, the link to Malan could not be proved.

He later gave evidence to the country's Truth and Reconciliation Commission, admitting responsibility for raids into neighbouring states, for setting up secret security networks, and for the deaths that resulted, but insisted these were "legal acts of state". The commission condemned his actions but the state's prosecuting authority decided it was not in the "national interest" to charge him or any of the other military brass.

Magnus André De Merindol Malan, soldier and politician: born Pretoria 30 January 1930; married 1962 Margot van der Walt (two sons, one daughter); died 18 July 2011.