"As far as irregular expenditure is concerned, this year we are reporting R49bn. Last year we reported just over R8bn," said Mohamedy.
"In terms of what we reported last year and what we report this year, this year you have the entire locomotives contracts all reported as irregular. They were not reported as irregular last year; they were instead reported as matters that we still needed to investigate.
"So if we look at the R49bn and the contracts included in it, there would be a fundamental difference with the R8bn reported last year. Therefore there is no direct correlation between the two numbers."
Mohamedy said this "misunderstanding" about irregular expenditure with the external auditors had led to their financial statements being qualified.
The National Treasury has also entered the fray on the disagreement between Transnet and the external auditors.
"On the issue of the difference of opinion, let us point out this issue came up very late in the audit process, in the last eight weeks," said Transnet acting chief financial officer Mark Gregg-Macdonald.
"It centres on the use of pre-qualification criteria on our tender. The view from the external auditors is that we were not supposed to use the pre-qualification on our tenders - saying that if we did, it made the tenders irregular.
"There are divergent views as to whether that is the case because we used the pre-qualification criteria to achieve the targets set by our shareholders around competitive supply.