Arms procurement parastatal Armscor told the Seriti Commission of Inquiry it was not involved in procurement of equipment bought in terms of the arms deal, SABC radio reported.
Acting general manager of acquisitions Dawie Griesel told the commission, sitting in Pretoria, that there was a deviation from standard policy procedures.
"Understandably Armscor would [normally] be responsible for the evaluation, but the defence department took over the process in this case," Griesel said.
He said an evaluations report was signed by a navy representative. Normal processes would have seen the Armscor programme manager sign it.
"Hence, the observation that no proof could be found of Armscor's participation," he said.
President Jacob Zuma appointed the commission in 2011 to investigate alleged corruption in the multi-billion rand arms deal.
The government acquired, among other things, 26 Gripen fighter aircraft and 24 Hawk lead-in fighter trainer aircraft for the air force as part of the arms deal.