The investigation comes after the High Court in Kimberley received an affidavit from the University of Pretoria's Centre for Child Law, containing allegations of excessive punishments and violations of children's rights.
The child law centre was submitted as a friend of the court in a case whereby Transnet is trying to evict the Noupoort centre from buildings that the parastatal owns. Transnet claims that the Noupoort centre owes R800 000 in rent.
In the affidavit, the Centre for Child Law reported on interviews it conducted with all 19 children at Noupoort.
It found that the children were not receiving proper therapy; that parents being forced to hand over guardianship to the centre; as well as that excessive punishments were being carried out, including instances where schooling, warm clothing and blankets were withheld.
On Friday, Judge Mpho Mamosebo ordered the department of social development to provide a report within 90 days on the children's circumstances.
Similar probes conducted in 2001 and 2002 resulted in the department deciding to close the centre. However, in both cases, the drug centre challenged the decision in court and won.