The DDR programme was set up in 2009 to help 180,000 former fighters in both the north and south to lay down their weapons and be re-integrated into society.
William Deng Deng, is head of the DDR commission in the south and is fighting for the audit to be released so he can confirm how much money has disappeared.
He believes the programme’s problems stem from mismanagement.
“There has been no boss. Who is the boss? Is it the UNDP, is it the donors, is it the government of South Sudan? It must be the government of South Sudan because this is a government project,” he said.
In response to charges that it siphoned off funds, the UN published a statement on Tuesday acknowledging that the programme faced "many challenges” and that senior management was taking the audit very seriously.
It also expressed concern about the low number of total former combatants who have been reintegrated.
Sudan's 22 year civil war, in which two million people died and four million were displaced, formally ended with a 2005 peace deal that offered the south a vote on secession. The independence referendum is scheduled for 9 January.