Nkonki Incorporated, the former external auditors, said in its audit report it was not able to verify more than R1bn in accounting adjustments in the 2010/2011 financial year, and could not express an opinion on the account.
Public Enterprises Minister Malusi Gigaba sacked the board of the state-owned airliner after a "severe breakdown" in the relationship between it and the minister, Gigaba's spokesperson Mayihlone Tshwete told SABC radio news on Tuesday.
The department told the newspaper this was "not a missing billion rand, it's a billion rand of disputes".
"We are not going to stop at anything to correct what has been damaged at South Africa Express, that is why the new board has been instructed to fix what needs to be fixed," Tshwete said.
"If management are involved in any wrongdoing and the Auditor General uncovers that, the minister will take steps... We will make whatever decisions are necessary."