The 16-day-old infant was grabbed from his mother's side in the village of Talabasta in eastern India, sparking a frantic search by police and 2,000 locals.
According to local media,the infant was sleeping under a mosquito net at his home in the eastern state of Odisha on Friday when he was taken by a rhesus macaque, a species with a reddish-pink face common across India.
The mother is saying that she saw a monkey take away her child. She raised an alarm but the monkey quickly leaped over the roof and vanished out of sight.
Family members then found the tragic infant at the bottom of a well on Sunday.
PC Pradhan said: "The baby was sleeping next to its mother when the monkey allegedly carried him away.
"He mother immediately raised cries for help but the creature fled with the baby and disappeared from her view."
He added: "We have registered a case of unnatural death and are getting an autopsy done.
"There are bruises on the child's left hand.
"The baby might have slipped from the clutches of the monkey, and died after falling into the well."
Angry villagers and family members staged protests outside the forestry department demanding measures to contain the growing monkey population in the region.
PC Pradhan said there was a "big monkey menace" in the area.
Activists say the invasion of the animal’s natural habitats by urban populations has caused the problem.
He added: "They snatch eatables from passers-by or troop into homes, open fridges and steal food items.
"Right at this time there are 20-25 monkeys sitting on the roof of my office."
Animal protection activists say depleting forest and natural cover has forced the primates to move into human habitations and forage for food.
No case was registered as the "family is convinced it's the monkey that killed their child".
In March last year, schools were closed in Odisha's Kendrapada district because of frequent monkey attacks.