New York State Police are shedding more light on why an Amber Alert was not issued in the case of 2-year-old Jovani Ligurgo and his father John Ligurgo, who were found dead Wednesday in a burning car with gunshot wounds.

Jovani Ligurgo went missing Tuesday afternoon while in his father's care. His parents were in the middle of a custody battle and a court hearing was scheduled for Thursday.

John Ligurgo didn't return Jovani to his mother when he was supposed to, according to a court visitation schedule. He then allegedly set fire to his Coram condo before disappearing with his son and a rifle.

Suffolk Police Commissioner Geraldine Hart told reporters that the department asked state police to issue an Amber Alert, but that state police denied the request.

State police said an Amber Alert was not warranted based on the information provided by the Suffolk County Police Department.

On Thursday, News 12 asked state police for more specifics. A spokesman said that Suffolk police told state police multiple times during multiple phone calls between 8-9:30 p.m. the night Jovani disappeared that they did not believe the child was in any danger.

That is despite an arson investigation at Ligurgo's home, an interview with the child's mother Maria Busone and having knowledge that the father may have had a gun on him.

According to state police, at 9:15 p.m., “SCPD advised they interviewed the mother, and still had not developed any further information that led them to believe the child was in danger or back in New York, and they were continuing to treat this as a custodial interference case.”

At 9:30 p.m., state police decided no Amber Alert was necessary. 

State police issued a statement Thursday afternoon: “As is standard procedure, both agencies will review the steps and guidelines ensure that best practices were followed. The Suffolk County Police Department and the New York State Police have worked closely on countless cases, and remain committed to continuing our close partnership."