The police have taken the boy's mother and her nephew into custody in connection with the incident.
The woman, a widow and mother of two including the deceased boy, has been arrayed as the second accused in the case.
The boy’s paternal grandfather, Babu, had approached the Thiruvananthapuram CWC to secure the custody of the young one.
The three-year-old boy, who was allegedly assaulted by his mother and undergoing treatment at a private hospital near Aluva, succumbed to injuries on Friday morning.
It was found the boy was beaten with a wooden object and there were burn injuries on several parts of his body, police had said.
The child, who underwent an emergency surgery to arrest internal bleeding, remains on ventilator support. According to doctors, the boy was found with multiple bruises on both his lower limbs.
The Kalpakanchery police on Monday arrested six persons for sexually abusing five minor boys in Malappuram.
Seven-year-old boy who was assaulted by his mother's partner in Thoduppuzha was laid to rest.
The boy's mother's partner had murder charges dropped on him with evidence suggesting the boy had been tortured earlier also.
Justice Devan Ramachandran on April 1 had sent a letter to the Chief Justice inviting attention to the inhuman torture of two minors.
A detailed statement of the child, who is now with the relatives, will be recorded by the Child Welfare Committee.
The Chief Minister has sought a report from district authorities of the assault on the boy who has less chances of recovery.