Authorities arrested 27-year-old Allen Shannon on second-degree murder charges in the death of Anniyah Levant.
According to medical examiner's report, the toddler died of blunt impact injuries to her body and head.
She also suffered fractures and internal injuries.
Investigators say the mother initially told doctors the little girl fell off a bunk bed in their apartment in Corona, Queens.
Friday night, the medical examiner confirmed that the death was indeed a homicide.
"The injuries to the baby are inconsistent with that type of event so obviously we're investigating," said NYC Police Commissioner Ray Kelly.
The mother of 19-month-old Anniyah told doctors her daughter fell from a bunk bed.
She took the unconscious child to Mt. Sinai Hospital Tuesday afternoon.
But, investigators say her little body had signs of child abuse, not a fall.
Sources say Anniyah had a broken jaw, a collapsed lung, and bruises on her face.
"I've never seen anything out of the ordinary. I wish I would have so I could have alerted someone before this ever happened," said Sylvia Lopez, a neighbor.
The little girl's death happened in close quarters making it really hard for neighbors who are used to seeing the little girl come and go everyday.
"I feel so bad for the baby, so bad. She was just a little girl. I don't know what was the reason for all of this," said Lopez.