The factory in Rajouri Garden area in West Delhi was also sealed and its owner was apprehended, police said.
"Assistant Commissioner of Police and the local SHO was part of the team which rescued thirteen children from a factory here today," said Deputy Commissioner of Police (West) Ranvir singh.
Two of the boys, aged between 12 and 17, belong to Nepal while the others had been trafficked from Navgarh village of Siddharth Nagar district in Uttar Pradesh, said another police official.
The children said they were forced to work for 15 hours a day up to midnight for a meagre pay.
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"We lived here itself and never moved out. We ate and slept together," said one of the rescued child who is a resident of Nepal.
The medical examination of these children revealed a high level of malnourishment.
The complaint was filed by NGO Bachpan Bachao Andolan (BBA).
All the children were sent to the DonBosco rehabilitation home on directions of the Child Welfare Committee.