TRC investigative unit head Dumisa Ntsebeza wanted to know whether an article on Swapo brutality had been planted in the magazine as part of the SA Defence Force's bid to discredit the liberation movement.
Ntsebeza said the commission had information that a special unit comprising white soldiers had been used to carry out massacres in an attempt to protray Swapo as "murderers killing their own people".
The soldiers would blacken their faces, don Swapo fatigues and arm themselves with Ak47s before attacking settlements of Swapo sympathisers at dawn.
"The media would then be called to the scene," he said.
Malan replied: "I would like to see that Scope ... to read it."
He said he knew little about SADF "disinformation operations" but would not have supported one as described by Ntsebeza.
If the SADF had been exposed as the true perpetrators of the atrocities then South Africa would have lost the war in the territory "hands down".
"I do not know who authorised such operations. If we did, it was totally against the argument of winning the hearts and minds of the people. At that stage we were busy with civil affairs and trying to help people help themselves."