The boy had gone missing from a slum in Okhla Phase II on September 27, a senior police officer said.
Rohit (19) allegedly killed the boy on Wednesday, Romil Baaniya, Deputy Commissioner of Police (Southeast), said.
The accused hid the body in a box bed. He later stuffed it in a sack, which was found near the boy's house this morning. Some locals informed police on noticing the strong stench.
On finding "Rukmani" written on the sack, a shopkeeper in the area told police that Rukmani's son Rohit had purchased flour from him in that bag, Baaniya said.
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Rohit went into hiding and switched off his phone, police said.
He was arrested today.
During questioning, Rohit told police the boy would peep into his bathroom and pass lewd remarks at his wife.
He told police that the boy's father had also abused him once in front of his wife.
Asked if he sexually assaulted the boy, Rohit replied in the negative, police said.
Police are awaiting the post-mortem report, said the DCP.