The Crime Branch sleuths arrested Krishnanarayan Yadav (22), Tausif Ali Taufik alias Shaikh (24) and Mehmud Ali Sadaf alias Sayyad (22) last night, an official said today.
The trio were produced before a local court which remanded them in police custody till January 22, he added.
Highly-decomposed body of the boy was spotted lying in a pit on December 24, 2015 by some labourers who were laying cables at the spot.
According to police, the trio allegedly kidnapped the minor sometime in October last year from a Wadala slum after luring him with sweets.
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A case of missing person had been registered by Wadala TT Police in this regard.
Later, the boy was identified by his parents on the basis of his clothes.
The accused persons are residents of Wadala and Antop Hill areas in the city.