South Africa's National Prosecuting Authority (NPA) said Transnet's former chief executive officer Brian Molefe and finance chief Anoj Singh were among four people held in connection with a multimillion-dollar corruption case.
"Several arrests of former Transnet executives have been effected this morning, through arrangement with their legal representatives," the NPA said in a statement.
The arrested appeared before a court in Johannesburg on Monday and were granted 50,000 rand (about $3,000) bail.
An NPA spokesperson confirmed to AFP the executives are facing charges of fraud and breaching public finance regulations, linked to a 93-million-rand corruption and fraud case surrounding the 2015 procurement of more than 1,000 locomotives.
Transnet owns all South Africa's rail, ports and pipelines -- the logistical backbone of the continent's most advanced economy.
Lawyers for Molefe and Singh said their clients intended to plead not guilty.
A report into state graft under Zuma published earlier this year described Transnet as a "primary site" of state corruption.
The investigation led by Chief Justice Raymond Zondo, found more than 41 billion rand in contracts had been "irregularly awarded for the benefit of entities linked to the Gupta family," a business family of Indian migrants with close ties to Zuma.
The opposition Democratic Alliance party welcomed the arrests, saying they hoped they were the "beginning of justice".
"While others have already been charged in this case, it seems that the last chickens have now finally come home to roost," the party's senior lawmaker Glynnis Breytenbach said in a statement.