The victims, mostly minor girls allege that they were beaten up, paraded naked and sexually exploited by the caretakers of the facility.
The shelter home is located at Rohtak in Haryana and it is run by an NGO.
The disturbing events came to light after a team of the National Commission for Protection of Child Rights conducted a surprise raid on the home on Wednesday night.
The operator of the shelter home has been arrested and the police have registered a case against the accused, said a news report.