The toddler's body was found by Tadepalli police on the banks of Krishna river in the early hours today, they said.
The boy, Bodapati Moksha Tejagna, who lived with his grandfather Rambabu, an assistant sub-inspector of police at Ponnur, had gone missing last evening after his paternal uncle Hari Krishna (the brother of the boy's father) took him away, an inspector at Tadepalli police station said.
Later, a missing complaint was filed at Ponnur police station, Rambabu said.
However, the motive behind the killing is yet to be ascertained, police said.
The boy's father works as a software engineer at an IT firm in Hyderabad.
A search has been launched for the boy's uncle, police said, adding further probe is underway.