Amina Okpara, 49, who is from Cameroon and married to a Nigerian, is facing charges of defeating the ends of justice, fraud and corruption.
She was arrested on June 14 after a sting operation carried out by the Hawks and two days after the orphanage was shut down and 17 children removed.
Hawks spokesperson Philani Nkwalase said it was alleged that the accused had redirected donor funds for the welfare of the children and centre operation into their bank accounts.
During her second appearance, prosecutor Adiel Jansen said: “We have received information that the accused is planning to skip the country. (Because) she is a flight risk and her existence in South Africa is based on fraud, it is submitted that she not be granted bail.”