Judge Ronel Tolmay has rejected Myeni's application to change her plea in the High Court in Pretoria.
Myeni wanted all SAA board members who worked with her to bear joint responsibility for what happened at the airline.
However, the judge did not agree with this.
Tolmay said errors in Myeni’s arguments should be fully explained.
Her lawyer Ncebayethu Buthelezi had argued that her previous lawyer did not do his work properly, but Tolmay disagreed.
Myeni was taken to court by the Organisation Undoing Tax Abuse, saying that during her tenure at SAA, the airline lost billions of rand as a result of her poor management style.
The main hearing is due to begin next month.