Observing that it was a 'serious issue' which requires thorough investigation, a division bench comprising Chief Justice Manjula Chellur and Justice P R Ramachandra Menon granted the government time till July two to place all details in a sealed cover.
The direction was issued on a PIL seeking CBI probe in the case.
Advocate General K P Dandapani claimed that Kerala government had taken all steps to protect the interests of the children.
The bench did not consider the pleas of Association of Orphanages, which claims to have 1800 orphanages under it, and the orphanage at Mukkam, to implead them in the case.
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The counsel for Mukkam orphanage stated the children were studying there and they had gone home for summer vacation.
The bench reiterated that sending away children will not solve problems. "They were brought like chicken", the judges held.
At least 580 children from three eastern states being brought to two orphanages in Kerala were detained by police at Palakkad railway station early this month on finding that many of them did not have proper documents.
The issue had snowballed into a major row in the state with IUML, key partner in the ruling 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.