The State capture inquiry has recommended that police further investigate former Transnet executives Brian Molefe, Siyabonga Gama and Anoj Singh with a view to prosecuting them for offences that include graft and fraud.

The inquiry chaired by senior judge Raymond Zondo was established in 2018 to examine allegations of high-level graft during former President Jacob Zuma's nine years in power from 2009, after scandals and sleaze had overshadowed South Africa's politics for years.

The allegations levelled against Zuma include that he allowed businessmen close to him - brothers Atul, Ajay and Rajesh Gupta - to plunder state resources and influence policy, in what is referred to in South Africa as "state capture".

The Guptas and Zuma have denied wrongdoing.

Molefe, Singh and Gama also all denied wrongdoing when they testified before the commission.

The second instalment of the Zondo commission's report, seen by Reuters, focused on alleged corruption at state-owned freight logistics firm Transnet and the country's struggling defence company Denel.

Neither of the companies had any immediate comment.

Corruption at Transnet occurred between 2009 and 2018, accomplished primarily through the "Gupta racketeering enterprise" and those associated with it, the report said.

"State capture at Transnet involved a systematic scheme of securing illicit and corrupt influence or control over the decision-making," the report found.

"Corrupt actors" sought to gain control over staff appointments and governance bodies to influence large procurements and capital expenditure by changing procurement rules to alter the bid criteria to favour "corrupt" suppliers and pay inflated costs, it added.

These actors that include a small group of senior executives and directors "were strategically positioned to collude" in the awarding of contracts such as multi-billion rand locomotive tenders that were often unfairly given to certain suppliers linked to the Gupta enterprise.

The report identified Molefe, Singh and Gama as the "primary architects" and implementers of State capture at the freight company.

The allegations levelled against them and others include accepting cash bribes from the Guptas at their Johannesburg compound between 2010 and 2018, contravening the Public Finance Management Act to favour bidders associated with the Gupta enterprise, inflating contract prices and money laundering.

On Denel, the report found that the contracts Denel awarded a Gupta company were all "irregularly awarded" and in breach of the constitution.