The Auditor General found the Defence Ministry racked up nearly R800-million in irregular expenditures during the 2010/11 financial year.
On Tuesday, Minister Lindiwe Sisulu reported to Parliament's Portfolio Committee on Defence on her department’s audit.
She told the committee that the irregular expenditure was money spent without due process being followed.
Out of the 129 cases reported, 127 had been sorted out.
Sisulu said corruption was not necessarily at play.
The minister said her department was committed to achieving an unqualified audit by beefing up financial management systems.
Sisulu said her department needs a bigger budget.
Earlier in 2012, it emerged that the defence force has serious financial problems.
The department has also come under fire after President Jacob Zuma used two shadow planes to accompany his jet to New York back in January.
One shadow aircraft flew all the way to JFK Airport, while another flew half way.
The extra planes cost taxpayers around R10-million.