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"I don't know where they got this R99 billion figure. I don't know what calculation this is. I am baffled," defence ministry spokesman Siphiwe Dlamini commented on Monday about a report in The Star.
"The Auditor General has not even once given us a qualified report on that account. It has been unqualified since its inception in 1974."
The Star newspaper reported that it had calculated that the amount had been spent through the military account, which has a block on public access.
It reported that this was double the R49.6 billion that the AG told the Truth and Reconciliation Commission had passed through the account from 1974 to 1994.
Nearly R14 billion more was reportedly due to go into the account over the next two years.
Last week, The Star reported that Finance Minister Pravin Gordhan had exempted the Special Defence Account from sections of the Public Finance Management Act for three years.
The National Treasury said this was so the account would not have to publish separate financial statements and disclose spending details.
According to the newspaper, the account is for buying weapons and equipment, funding covert activities, and spending on the arms deal.
Dlamini said it was gazetted by law and managed by the defence department and national treasury. Certain aspects of it were not for public consumption, he said.
"When we procure equipment for the defence force, it happens sometimes over a long period of time. There's nothing secret about it," he said.
"That account allows us to use money we have budgeted for... and if the item or equipment is not available at that specific time, we keep the money until the item is available.... That may sometimes take two to three years."
