The unit had been forced to terminate the contracts of part-time staff, he said in Cape Town after a briefing to Parliament's portfolio committee on justice.
At present, the SIU had to make do without about R175 million that is due to it from state entities, leaving R307 million that was directly allocated from National Treasury for this financial year.
"Our budget consists of these two components. That part is being held back, so we do have serious cash flow problems," he said.
The funding shortfall has come about after Eskom pointed out last year that the unit's founding statute did not expressly allow it to invoice state entities for the investigations it conducts.
Head of investigations Gerhard Visagie said: "We sought legal opinion and in fact it was confirmed that we are not allowed to bill state institutions. We had been openly doing that for seven or eight years.
"It was rather catastrophic for us. It cut 35 percent out of our budget."
Visagie said the unit had given notice to some 100 consultants that were working alongside the unit's 600 permanent members.
"May 4 or 5 will be their last day. We hope that the issue can be addressed because ... it is going to seriously affect our capacity."
He said the unit urgently needed an amendment to the legislation to allow it to take remuneration from departments and hoped it would be in place by October.
The SIU's budget was increased by 2.3 percent in 2012/13, amounting to a reduction in real terms.
MPs from across the political spectrum expressed shock that the SIU's allocation was four times smaller than that of the Public Protector.
Said ANC MP John Jeffery: "I'm not comfortable with this. It is not the same role, these people are collecting money."
He was referring to the misspent state funds the SIU recovered in the course of its work.
The workload of the unit has increased significantly after it received seven new proclamations in recent months, and three long-running investigations were extended.
Among these is a probe into procurement practices in the police force, which was pointing to irregular spending of up to R1.5 billion.
Head of strategy Zola Ntolosi said: "There are definite indications of irregularity in this regard and this will probably produce significant results."
The former head of the SIU, Willie Hofmeyr, estimated last year that up to R30 billion in state funds was lost to corruption annually.
The unit said on Friday this estimate still held true.
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