With her in the dock were co-accused Patience Thandeka Mahoti and Thabisa Lucilia Delo, also charged with tax fraud.
All three were arrested on Wednesday, and appeared before magistrate Cyril Kroutz soon afterwards.
Tax fraud prosecutor Freek Geyser told the court the current fraud charge involved R800,000, but that the investigation was only at the beginning stages.
There were likely to be many more fraud charges added, he said.
They were released on R1500 bail each, and warned to appear in court again on April 9 next year.
The charge sheet alleges that Timakwe and Mahoti, whilst in Sars’ employ, manipulated the electronic system to fraudulently generate tax refunds for “clients”.
Timakwe has since been dismissed, while Mahoti is under suspension from her job.
It is not yet known what Delo’s alleged involvement was.