The Department of Defence had spent R34.4-million on flights for senior government officials, but nobody was on board.
This was revealed through Parliamentary questions about "ferry flights", where aeroplanes are chartered to collect VIPs.
"Parliamentary questions revealed that between 2009 and 2012, the South African Air Force (SAAF) undertook a total of 700 ferry flights for VIPs at the cost of R34.4-million," said Democratic Alliance (DA) shadow minister of defence David Maynier.
President Jacob Zuma's business jet, Inkwazi, undertook 58 such flights at a cost of R4.9-million.
The ministerial handbook allows officials to ask for chartered flights in exceptional circumstances, where regular scheduled flights cannot be used.
Maynier called on the department to improve its scheduling and planning.
"The fact is that we are wasting millions of rand on hundreds of empty VIP flights."
It is not clear which ministers used the planes, but the DA said it would submit follow-up Parliamentary questions to Defence and Military Veterans Minister Nosiviwe Mapisa-Nqakula.
It will ask for the names of the ministers "using and abusing" the service.