The remains were discovered after a search warrant was executed at the home of the child's mother, Heather Kowalczik and her husband, Robert Rodriguez.
Police initiated the search after an Amber Alert was issued Friday for the couple's son, 9-year old Robert Rodriguez, Jr.
The boy was found and is okay.
However, the focus of the investigation then turned to the couple's home on Hallock Street in Farmingdale.
Police confirmed that they were investigating the possible murder of a child who would now be 3-years old, and that the suspect is Robert Rodriguez, the father of the 9-year-old.
Investigators say the 3-year-old had not been seen in at least a year. That is about how long the family has lived in the home, according to the landlord.
According to neighborhood residents, a family of four lived there, including Robert Rodriguez, Sr., two children and his wife. Eyewitness News' camera spotted Rodriguez's wife in the front seat of a police vehicle leaving the scene.
When neighborhood resident Meade Jackson was asked how she would describe the Rodriguez', she said that they were a nice family.
Investigators tell Eyewitness News that the investigation began after a tip from state police in Middletown, New York.
Authorities say the family never reported the child's death.
Investigators are still trying to determine how the child died, and why the family kept it a secret.
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