Orange County Sheriff’s Office spokeswoman Rose Silva said the two-year-old boy was dragged underwater by an alligator at Seven Seas Lagoon.
Authorities have declared the search as a recovery effort.
The Nebraska family were on holiday at the Grand Floridian Resort and Spa in Florida with their three children and were relaxing on the shoreline when the attack happened.
Sheriff Jerry Demings of Orange County told local media that the child was in a play pen near the water when the gator attacked.
“They had a child in a baby play pen and waiting at the lakes edge when the alligator attacked the child,” Sheriff Demings said.
The father ran into the water and wrestled with the animal to save his son but he in vain.
The boy’s mother then attempted to save her little boy but was also unable to free him and the family alerted a lifeguard.
Witness then called 911 to say a child had been attacked by an alligator and deputies have been scouring lake since.
More than 50 law enforces and two marine rescue boats will continue to search the waters along with helicopters that have light beams, sonar and a dive team.
A Walt Disney spokesman told the press conference: “Everyone here at the Walk Disney world resort is devastated by this tragic accident.
“Thoughts are with the family and we are doing everything we can do help them.”
Adrian Whitsett, a reporter for WESH Orlando, tweeted that the alligator is approximately 2.1 metres long.