"The superintendent of children home in Lajpat Nagar Ram Sahay Meena was arrested on a complaint received through Delhi government official last evening," a senior police officer said.
Meena was sacked along with another staff of the facility on the orders of Delhi Women and Child Welfare Minister Sandip Kumar.
"Some girl inmates revealed that they were molested and raped by Meena. They were sent for medical examination and rape was confirmed in a few cases," the officer said.
The incident had come to light after Kumar's visit to the home and his meeting with the girls on June 3.
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After consulting the Child Welfare Committee (CWC), the minister had asked them to lodge a complaint against the superintendent under the provisions of Protection of Children from Sexual Offences (POCSO) Act.
The minister had ordered termination of Meena and a woman welfare officer who was also allegedly involved in misbehaving with the girls.
It was reported to the minister that the superintendent had allegedly taken minor girls to an isolated room and tried to physically abuse them.
Police said they are also questioning two more staff members of the facility who are likely to be arrested.