Ankur Gupta (42), the caretaker of the NGO, Drone Foundation, and accused of allegedly raping two HIV+ minor girls was produced in a court on Friday.
He has been sent in two-day police remand.
Gupta, who is also reported to be HIV+, will be produced again in the court on Sunday.
The police have sought his remand to interrogate him and extract more details into the rape incident, alleged to have taken place at his Bhondsi-based child shelter.
Sunita Gupta, his mother and co-accused on the charges of conspiracy, was not arrested.
The NGO housed 14 HIV+ children, including eight girls.
A team of the National Commission for Protection of Child Rights (NCPCR) had raided the NGO on Tuesday and filed a criminal complaint on the statement of two minor girls. Meanwhile, all the children have been moved out of the NGO-run shelter.