Nakira Griner is charged with murder and other counts in the death of 23-month-old Daniel Griner Jr.
Prosecutors have said the woman initially reported that her son had been abducted Friday night.
A response team began a search aided by city and state police, prosecutors, and bloodhounds from New Jersey State Park Police.
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The child's burned and dismembered remains were found around 3 a.m. Saturday, buried under a shed in the yard of Griner's home.
Griner told police she hit the boy because he wouldn't "eat nor listen to her," according to the criminal complaint.
The complaint said Griner admitted striking the child so hard that she left bruises on his face and also said he fell down a flight of stairs.
After striking the child, she didn't call for help, but placed him in a stroller and left him alone, according to police.