The process of the Seriti Commission, which found that there was no evidence of corruption in the "arms deal", was flawed, the Gauteng High Court in Pretoria heard on Tuesday.
"We know that there is a constitutional obligation to combat corruption and to combat it, is to expose it.
"The commission was set up to find out if corrupt activities took place in the arms deal and found that there was none. However, the commission did not investigate properly," advocate Geoff Budlender, SC, argued on behalf of organisations Right 2 Know (R2K) and Corruption Watch (CW).
The two civil society groups are challenging the findings of the commission, which was set up by former president Jacob Zuma in September 2011.
Zuma appointed Supreme Court of Appeal Judge Willie Seriti as the chairperson of the commission.
It was tasked with investigating whether there was any improper influence in the awarding of contracts in the Strategic Defence Procurement Package (SDPP).
This became known as the arms deal which led to the government acquiring, among others, 25 Gripen fighter aircraft, 24 Hawk lead-in fighter trainer aircraft for the SA Air Force, as well as frigates and submarines for the SA Navy, News24 earlier reported.
The commission began its hearings in August 2013.
Budlender highlighted several "topics of failure" in the manner in which the commission gathered and considered relevant material and evidence.
In his heads of argument, Budlender also stated that the commission failed to consider two thirds of documents from the Scorpions and the Hawks.
"The commission received an internal hard drive containing approximately 1.3 million pages of documents relating to the criminal investigations.
"This was one third of the documents in the containers which were deemed relevant to the commission's investigation. The commission did not consider the remaining two thirds of the documents," he said.
In addition, the commission did not access and consider relevant records of criminal proceedings, Budlender added. He was referring to matters raised in the Schabir Schaik trial as well as the investigation and criminal proceedings against Zuma.
The one-time financial advisor to Zuma was released on medical parole on March 3 2009, after serving just more than two years of a 15-year sentence for corruption.
Shaik was convicted of two counts of corruption and one of fraud, relating to his facilitation of a bribe, allegedly paid by a French arms company to Zuma.
Budlender further highlighted how evidence from key witnesses, such as advocate Fana Hlongwane and Chippy Shaik, wasn't tested.
Both parties submitted evidence denying any wrongdoing and: "The commission as well as its evidence leaders failed to put forward questions or allegations to the witnesses."
The Presidency, which is one of the respondents in the matter, is not opposing the application and further submitted that they are "abiding".
"The findings are what they are," Nazieer Cassim, SC, appearing for the Presidency, told the court.
Cassim told the court the commission failed to interrogate evidence brought before it.
"They did not investigate the evidence.
"If this commission was serious about its functions, it would have made serious findings about corrupt activities in the arms deal," he submitted.
Judgment has been reserved.