The Al-Noor Orphanage has also denied claims by the department that the children suffered “physical and sexual abuse” at the premises.
It clarified that 16 and not 17 children were taken away by DSD officials this week.
The department said following an investigation, the children have been removed and placed in other child and youth care centres, and are being assessed and counselled.
“Criminal charges have also been laid with the SAPS against the alleged perpetrators,” said DSD spokesperson Esther Lewis.
Police did not respond to queries about the matter on Thursday, and it’s not clear who the alleged perpetrators are.
DSD officials have also suspended the centre’s registration, pending the outcome of the investigation.
The orphanage has confirmed the children, who were removed, are between the ages of eight and 16 years old.
On Thursday, no children could be seen at the orphanage.
Queries to management were referred to their lawyer, Luvuyo Twalo, who was at the premises for a meeting.
According to him, the police have not been to the facility and no one there has been questioned about the matter yet.
“These allegations are untrue and we will be going to court. We are also trying to get answers from the department,” Twalo tells the Daily Voice.
“My clients were not informed how or where these allegations come from.”
In a statement on Thursday, the orphanage said DSD officials had no regard for the children.
“The department failed to inform the children about the process and their removal, and they forced them to take all their belongings,” Al Noor said.
“That process was not child-friendly, thus not in the interest of the children, thus violating the children and traumatising them.
“The home was not issued with any tangible reasons nor notice of removal. The management of Al-Noor made several attempts to communicate with the department with regard to a plan of action and to urge that due process be followed.
“The department promised to send communication to the home, but instead decided to forward misleading information to the media without even meeting the home.
“The children are currently placed in juvenile delinquent centres, places where drug addicts and children at risk who are dangerous are placed.
“These allegations are malicious and unfounded as they have not yet been put to test.”
In 2006, DSD officials found the facility was operating illegally and that prostitutes were working from the premises.
It was also found that Nolundi Ebi, a former Home Affairs employee, used contacts in the department to arrange birth certificates and other identity documents for the children.
These documents were then allegedly used to apply for social grants on behalf of the children, mainly from Langa, Gugulethu and Khayelitsha.
Many of the children were found not to be orphans.