The incident took place at Gandipet village on the outskirts of the city.
E Ramulu, a labourer, made his wife drink toddy with him last night.
After she slept, he picked up the baby girl and threw her into a well in the nearby field and then returned to his bed, police said.
In the morning, Ramulu played innocent and asked his wife about the baby and started a search.
But the villagers suspected that something was fishy, and questioned him.
Finally he confessed to the act. He also showed the well to villagers before fleeing from the spot.
The girl's body was later retrieved from the well, police said.
The couple already had a 3-year-old girl and he badly wanted a son when his wife delivered for the second time, police said.
Narsingi police have registered a murder case and are searching for him.