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Sydney Maree, the former chief executive of the NEF, quit his post on August 13 - the day on which an internal hearing was scheduled - following allegations of fraud against him.
According to earlier reports, about R1m disappeared from the NEF to "pay" Deutsche Bank for work that the bank had actually done free of charge. The money was reportedly traced to a personal account.
The matter was then reported to the Directorate of Public Prosecutions for further investigation. The progress of that probe is at this stage unclear.
On Friday, members of parliament's portfolio committee on trade and industry heard that "no money was lost, or taken" from the NEF.
"There has been problems with the CEO (Maree). We dealt with it quickly and decisively and no money has been lost," said Lionel October, the department's deputy director-general.
"When there was the allegations of fraud we immediately suspended the individual. We brought in the authorities to investigate and we also instituted a disciplinary action."
October said plans to appoint a new chief executive are in place, and a shortlist has been completed.
The NEF deals with loans of between R250 000 to R10m and falls under the department of trade and industry.
The fund was first announced in 1996 by Finance Minister Trevor Manuel, and was hailed by him as the government's tool for not only creating new wealth but for "creating millions of millionaires".
Maree is the former special adviser to Alec Erwin, the former trade and industry minister.
The fund's first chief executive, Khanya Motshabi, left in August 2003 amid rumours that he had been pushed to do so.
