President Cyril Ramaphosa has ordered the country's Special Investigating Unit (SIU) to probe allegations of maladministration at state run-power utility Eskom and logistics group Transnet, the government said on Friday.
Ramaphosa, who replaced former president Jacob Zuma in February, has made the fight against corruption a key plank of his administration as he seeks to restore investor confidence after the scandal-plagued Zuma era.
The announcement of the probe was published in the government gazette.
The SIU, which investigates malpractice in state institutions, state assets and public money, will investigate among other things, "unauthorised, irregular or fruitless and wasteful expenditure" incurred by Eskom and Transnet.
Eskom has been embroiled in allegations of corruption relating to a 1.6 billion rand ($130 million) contract that global consultancy McKinsey worked on with Trillian, a local company that was then controlled by Gupta family who are accused of using their access to Zuma to win state contracts.
Zuma and the Guptas have denied any wrongdoing
Transnet, which is also state-owned, has been investigating irregularities in the awarding of a 54 billion rand ($5 billion) contract to acquire locomotives in 2014.
Eskom spokesman Khulu Phasiwe said: "This matter has been a long time coming and we are happy that the SIU is starting this process."
Transnet was not immediately available for comment.