In its petition, Mukkam orphanage Secretary Dr Gafoor contended that the questioning by police caused much mental agony and stress to the children.
The petition is likely to come up for hearing before the court tomorrow.
Earlier, the court had directed the government to inform it by June 30 its stand on the PIL, seeking a CBI probe into the case filed by an NGO 'All Kerala Anti Corruption and Human Rights Protection council' of Palakkad.
The case has been posted to June 30 for government's reply.
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Over 580 children from Bihar, Jharkhand and West Bengal, meant to be brought to two orphanages in the state, were detained by police at a railway station in Palakkad early this month after it was found many of them did not have any proper documents.
The issue had snowballed into a major row in the state with IUML, the key partner in UDF,taking objection to treating the incident as a case of child trafficking.
The children are now kept at state-run juvenile homes of the Child Welfare Society in Palakkad, Malappuram and Thrissur.