Suparna Sethi, who heads NGO Suparna ka Aangan, and her employee Rachit Raju were sent to judicial custody by a local court today.
DCP (East) Maheshwar Dayal said Raju was arrested on charges of rape and Sethi for violation of Juvenile Justice Act as her organisation was not registered.
Raju, 20, was a cook and caretaker in the orphanage located at Wazirabad village in Gurgaon district where about 20 minors were lodged.
On the complaint of anther NGO Shakti Vahini, a team of National Commission for Protection of Child Rights had visited the orphanage yesterday when the incident came to light.
Dayal said Sethi might have been aware that Raju was raping and abusing the minor girls.