The court had on Tuesday dubbed the situation in the institute -- Adhyatmik Vishwa Vidyalaya -- located in north Delhi's Rohini as being "similar" to that witnessed in Gurmeet Ram Rahim's ashram in Haryana's Sirsa, but without making any direct reference.
An NGO has alleged that girls and women were kept at the "university" for 14 years and more.
While producing one girl in the court, who, the NGO claimed, had managed to get out of the premises, it alleged that she was raped during her stay there, which she has not even disclosed to her parents.
The NGO also alleged that girls confined at the ashram have committed suicide in the past, but the police never registered a case.
The raid, which went on until late in the night, saw the presence of Deputy Commissioner of Police (Rohini) Rajneesh Gupta, Delhi Commission For Women chief Swati Maliwal and a group of lawyers.
"We were also attacked in the ashram and held hostage for one hour," Ms Maliwal said.
She said that in the institute, letters about alleged sexual assault faced by the inmates, were found from a box and also certain injections and medicines were also found in huge quantities.
The Delhi High Court today directed the CBI to investigate the alleged illegal confinement of girls and women in the ashram where they were kept in "animal-like" conditions behind metal doors in a "fortress" surrounded by barbed wire.