"SA Express is not aware of a liquidation order that has been granted against the airline from Mothebe Shuttle Services," said the airline on Thursday.
This follows a media report to that effect.
The airline said while it had a R1.3 million annual contract with Mothebe, the contract has been flagged as irregular.
"Mothebe Shuttle Services is among the contracts that were identified by a recent forensic investigation as irregular," said the airline on Thursday.
The investigation also implicated SA Express procurement staff who were later charged with gross misconduct.
The airline has since opened criminal cases against those that have been implicated while the contract has been reported.
"Should Mothebe Shuttle Services proceed with the matter against SA Express, the airline intends to respond appropriately within the legal framework," said SA Express.
There was unauthorised scope and an irregular price increase on the tender.
"While the contract was for R1.3 million a year, SA Express was surprisingly charged R1.1 million for a period of four months from 1 December 2017 to 4 April 2018 which translated to R3.3 million a year, which was irregular," said the airline.