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The children, all aged between six and 17 years, are currently in the care of other relatives and the district Child Welfare Committee.
It was on Monday evening that the caretaker of the institution under the Child Welfare Committee realised the boys, all under the age of 15, were missing.
The caretaker of the institution realised the missing of the teenagers Monday evening.
The 13-year-old will be handed over to her parents on Monday.
The girl was rescued after residents heard her cries, said police.
There are also accusations that the police did not invoke the Juvenile Justice Act against her, which could lead to her losing her position on the CWC.
Police nabbed the accused in the case -- Hassankutty alias Kabir (50), of Ayirur in Varkala -- from Chinnakada in Kollam yesterday.
The police traced the woman and her two children to a camp of beggars in Coimbatore.
The Childline officers had rescued the minor from the premises of the railway station by 4.50 am. It is understood that the two are not Malayalis.
At the age of 10, Devika was rescued by the Child Welfare Committee (CWC) from a house in Kasaragod, where she was working as a domestic help.