On Monday, the body of Daksh Kanjode was found from the river here after local fishermen spotted it and informed the police.
The body was found dumped in the river wrapped in a plastic bag tied to a bucket.
A through probe into the crime led the police to the victim's step mother Lata Kanjode, who allegedly along with two other relatives killed the minor by strangulating him with a rope.
Apart from Lata Kanjode (35), her sister Varsha Jadhav (25) and sister-in-law Latika Jadhav (30) were arrested in connection with the case.
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According to the boy's maternal uncle, who lived nearby and had lodged a missing complaint with local police on July 9, the trio were often seen performing late night rituals but was unaware for their purpose and motives.
"We are now trying to find out if the boy's father was in anyway involved in the crime," said API M K Dhakane of Kalyan Railway Police.
Police had earlier registered a case under Section 363 (kidnapping) of IPC after the boy went missing.
Later, when his body was found a case under sections 302, 201, 120B and 182 of the IPC was registered, police said.
The trio was presented in the court yesterday and have been remanded into police custody till July 30, the officer said, adding that they are probing into the human sacrifice angle too.