The boys were presented before the magistrate and later moved to the care of Child Welfare Committee.
Three boys allegedly held captive at homes by their parents were rescued by the state's child protection services on Tuesday.
The boys - reportedly aged 6, 9 and 12 - have been handed over to the Child Welfare Committee on orders of Ernakulam District Collector Mohammed Y Safirullah.
According to complaints filed by neighbours, the children were kept confined to the house and not given elementary education.
The father, Abdul Lateef, in his 50s, told local media, "I do not believe in Indian rules and have been following the education system of Arabic countries for my children."
The father refused to allow anyone inside his house saying it was "holy and cannot be defiled with anyone entering it".
The three boys were presented before the magistrate and later moved to the care of Child Welfare Committee.
The children, however, defended their father saying they did not want to go to school and were happy with the education they were receiving at home.
"The neighbours have no clue who this family is. They haven't seen the three boys around except rarely. They live inside, on the second floor, in very mysterious conditions," an official said.