Johannesburg - President Cyril Ramaphosa has authorised the Special Investigating (SIU) to probe the affairs of the embattled SAA, the National Treasury and Eskom.
This was revealed in a government gazette that was published on Friday last week.
Ramaphosa said allegations have been made in respect of the affairs of the SAA.
He ordered that SIU investigate the procurement of the Airbus aircraft, legal services, and service providers for the SAA turnaround plan.
The president also said the SIU would also investigate maladministration in SAA’s travel rebate benefits for qualifying beneficiaries, payments made to vendors and implementation of procurement policy.
The SAA probe will investigate allegations that took place as far back as January 2002.
The National Treasury's multi-billion rand contract for information technology systems will also come under scrutiny.
In his proclamation, Ramaphosa said allegations have been made in respect of the affairs of the National Treasury.
He said the SIU should investigate the procurement and payments made for the Integrated Financial Management System (IFMS) in the manner that "was not fair, competitive, transparent, equitable or cost-effective".
The terms of reference for the SIU probe cover serious maladministration within the affairs of the National Treasury, improper conduct by officials, and unlawful appropriation for expenditure of public money, among others.
The SIU probe will probe allegations dating back to January 2016.
The National Treasury initiated the IFMS project, which was aimed to integrate human resource and financial management in government, in 2005.
It spent R1bn on the first phase and a further R1.2bn was spent on the second phase of the project.
A forensic investigation into the project found that the National Treasury flouted its own policies and regulations.
Ramaphosa also amended an Eskom proclamation to include probe into procurement coal, coal transportation services, diesel, cloud computing services, software licence and support services and engineering and project management consulting services, among others.
SIU head Andy Mothibi said the investigating body welcomed the gazetting of the proclamations.
"The SIU commits itself to execute the mandate set out in the proclamations and to investigate the allegations with integrity in order to deal with any corruption that might have occurred.
"We further commit to speed up the investigations to ensure that instances of maladministration, malpractice and corruption are reported, investigated, and those responsible are held to account and make sure the losses suffered by the state institutions are recovered,” Mothibi said.