The Progressive Preparatory School is not registered with Gauteng's education department, which it is obliged to do as a school, said the department's Nanagolo Leopeng.
Zanele Mngadi of the social development department said school had registered as a non-profit organisation in October 2006.
When registering, principal Caroline Lobi said her organisation's objectives were to provide numeracy, reading and writing skills to promote self-esteem and to engage children in sports and physical activities.
As a registered NGO, the school may not use any money it makes to pay members or office bearers for their services.
Leopeng said the education department was engaged in a campaign to warn parents and pupils about illegal independent schools "that may not meet the educational needs of the learners".