The Cape Town Magistrates' Court has issued an immediate warrant of arrest for the 26-year-old man who is facing various assault charges relating to the Al-Noor Orphanage Centre in Woodstock, Cape Town.
He was arrested in July on two charges of assault with intent to do grievous bodily harm, sexual assault and the sexual grooming of a child.
The centre's 49-year-old manager is facing charges of conspiracy to commit fraud and three charges of contravening the Immigration Act.
She is currently out on R5 000 bail.
News24 understands that the second accused is a senior staff member at the centre.
'I don't know where he is'
The Department of Social Development removed 17 children from the centre after allegations of physical and sexual abuse surfaced in June this year.
Appearing on behalf of the accused, advocate S Hlela informed the court that she had not seen her client prior to his matter being called.
A brief search by the court orderlies for the man confirmed that he was not present.
"I don't know where he is," Hlela said, thereafter acknowledging that the only course of action would be to issue a warrant of arrest.
His warrant of arrest was signed off by the court. His bail, in effect, was withdrawn.
The matter was postponed to October 11.
*This story has been updated.