The child was admitted to a private hospital at Kattappana near here yesterday with serious injuries.
With the incident coming to his notice, Chief Minister Oommen Chandy asked the district authorities to submit an urgent report on the incident.
Police took into custody the boy's father and stepmother based on details gathered from the private hospital.
The couple had initially said the injuries were the result of a fall, but the doctors who examined the boy ruled that out and informed the police of the incident, police sources said.
After the death of the child's mother a few years back, his father had married another woman.
