EMBED >More News Videos Joe Torres reports on the questions over why an Amber Alert was not issued.

CORAM, Suffolk County (WABC) -- Police believe they have found the bodies of a missing 2-year-old Long Island boy and his father.A vehicle with the matching license plate of 43-year-old John Ligurgo III has been found in Rockbridge County, Virginia with two bodies inside. They are believed to be the bodies of John Ligurgo III and his 2-year-old son, Jovani Ligurgo.Suffolk County police began searching for the pair after Jovani's mother reported him missing when he wasn't dropped off at her home in Smithtown on Tuesday afternoon as planned.About an hour earlier, there was a fire at John's home in Coram. Police say two beds had been set on fire inside the home.Jovani's mother went to the home when she heard about the fire and spoke with detectives and informed them she believed John had a gun inside the house.Police looked for the gun but discovered it was missing.Toll cameras captured his black Jeep Grand Cherokee crossing the George Washington Bridge into New Jersey. The SUV had New York plates GAV4699 -- the same plates on the vehicle found in Virginia.Suffolk County police said they asked state police to issue an Amber Alert."We followed protocol, we provided the necessary information and details to the state police and at that time they made the determination not to issue the Amber Alert," Cmsr. Geraldine Hart with the Suffolk County Police said.New York State Police released the following statement about why an Amber Alert was not issued:----------