The findings of the Seriti inquiry into the multibillion-rand arms deal, which ran for four years and cost nearly R140m, have been set aside by the Pretoria high court.

“Based on the uncontested evidence presented to this court, the commission failed manifestly to inquire into key issues, as is to be expected of a commission,” judge president Dunstan Mlambo said.

In a unanimous ruling, Mlambo and two other judges have granted an application by non-governmental organisations (NPOs) Corruption Watch and Right2Know to invalidate judge Willie Seriti’s findings that there was no evidence of corruption in the arms deal.

“It is clear that the commission failed to inquire fully and comprehensively,” Mlambo ruled on Wednesday morning, adding that the inquiry also failed to confront or properly question witnesses implicated in arms deal corruption, including arms deal adviser Fana Hlongwane and former head of acquisitions in the arms deal Chippy Shaik.

“The commission also accepted the evidence of Mr Shaik without demur,” he said, adding that Hlongwane had not even been questioned by the inquiry, despite damning evidence against him. This amounted to a “manifest failure” to properly question Hlongwane, he said.

President Cyril Ramaphosa, and Seriti himself, did not oppose this application, effectively meaning that the state made no attempt to defend the inquiry.

Former president Jacob Zuma, who appointed Seriti to investigate the arms deal in 2011, had used his findings as part of his court bid to have his arms deal corruption case permanently stayed. Zuma stands accused of accepting a R500,000 bribe from French arms company Thales, facilitated by his former financial adviser Schabir Shaik, in exchange for his protection from any potential arms deal inquiry.

Mlambo on Wednesday morning pointed out that the Seriti inquiry had refused to examine Shaik’s trial record, for reasons that were not entirely clear.

Zuma appointed Seriti to investigate allegations of corruption and fraud in the R46.7bn arms-procurement deal initiated in 1999, in which navy frigates, fighter jets, submarines and helicopters costing billions of rand were purchased by SA.

Seriti dismissed claims of corruption in the arms deal as “wild allegations with no factual basis” and “baseless hearsay”. Corruption Watch and Right2Know argued that Seriti had, however, failed to fulfil his mandate, as he failed to properly investigate evidence of alleged arms deal corruption.

Corruption Watch further claimed that of the 4.7-million pages various authorities had collected in evidence related to the arms deal over the years, only 1.3-million were scanned and used in the inquiry. It argues that the inquiry had access to shipping containers of evidence it never assessed.