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," police sub-inspector S.M. Baral told AFP.
"We launched a search along with the forest officers. Yesterday (Sunday) the baby was spotted inside the well dead," she told AFP.
A post-mortem showed the infant died of asphyxia due to drowning, Baral said.
"Since there were no injury marks on the baby, maybe the monkey dropped him in the well."
No case was registered as the "family is convinced it's the monkey that killed their child", the officer said. The incident happened in the village of Talabasta in Cuttack district.
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Media reports said monkeys have become a growing nuisance in the area where the child was taken.
In March last year, schools were closed in Odisha's Kendrapada district because of frequent monkey attacks.
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The same month a government employee died from head injuries after a monkey leapt at him from a tree, the daily reported.
Though revered in the majority Hindu nation, monkeys are a menace in many cities, trashing gardens and office and residential rooftops and often viciously attacking people for food.
Activists say the invasion of the animal's natural habitats by urban populations has caused the problem.
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