Former Free State Department of Agriculture head Peter Thabethe failed to clarify a payment of $5m for a feasibility report on the Gupta-linked Vrede dairy farm project during testimony at the state capture inquiry.
The amount paid to Gateway Trading converted to roughly R49m.
On Monday, Thabethe said he believed the payment was to the tune of R30m.
However, evidence leader, advocate Leah Gcabashe begged to differ.
"You told us that the R30m paid in July 2012 was for the feasibility report, but it was taken out of the country and it was said to be reserved for equipment - so let's not get confused. You know it was taken out of the country because it was said to be reserved for orders," she said.
In a previous appearance before the commission, Thabethe could not explain why he allowed R29m of R30m to be removed from the account. But he indicated that the money was reserved for equipment that was yet to be manufactured for the project, News24 reported.
Thabethe responded: "I do not agree with the statement that says I know that money was taken out the country. What I know is that on this document in January 2018, the work that was expected was delivered and I signed off. This is what the money paid for."
"What happened to the money? I do not know," he added.
It appeared to the state capture commission of inquiry, chaired by Deputy Chief Justice Raymond Zondo, that Thabethe was conflating two separate payments relating to the Vrede dairy farm project: The $5m for the feasibility report paid to Gateway Trading (linked to the Guptas) and the R30m which was reserved for equipment.
"I am forced to draw conclusions from the record as it stands because we cannot stay on one point all morning," Gcabashe said.
Agricultural economist Andries Maree, who provided an analysis to the commission, called the feasibility report/study "a desktop, copy and paste report", which appeared to be a document on farming rather than a feasibility study, News24 reported.
The controversial project was created so that 100 black emerging farmers would receive five cows each as part of an empowerment scheme.
Gifted to Estina in 2013 under a free 99-year lease by the provincial Department of Agriculture, the farm was one of the most controversial transactions between the Guptas and a government entity, News24 previously reported.
The inquiry continues.