According to police, these children had been brought to Kerala illegally and lodged in an unauthorised orphanage. They would be sent to their home states in the next three days with the government making arrangements for the travel.
The children, majority of whom were from Jamtara in Jharkhand, had been shifted to a state-run children home.
A police team and Social Welfare officials would accompany the children during the journey, police said.
Officials found that the orphanage had been functioning "illegally" and children lodged in unhygienic conditions.
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The bringing in of children from eastern states to orphanages in Kerala without following legal procedures has become a major issue after railway police detained over 500 children from Jharkhand, Bihar and West Bengal, who travelled without proper documents, at Palakkad last month.
The issue had snowballed into a big controversy, bringing orphanages run by charity trusts under the scanner. A case was registered and 10 person who accompanied by them had been arrested.