Orange County Sheriff's Office spokeswoman Rose Silva said the two-year-old boy was snatched and dragged into the Seven Seas Lagoon about 9:30pm on Tuesday, local news outlets reported.
Deputies were continuing the search for the child and local authorities called in the help of an alligator trapper.
A police official said that the father of the boy entered the water and tried in vain to grab his son as the alligator dragged him into the lagoon.
"At some point the mother may have also entered the water, so the parents diligently tried to get the child," the official said.
The family of five was holidaying from Nebraska and were out relaxing at the beach area of the lagoon. The father and child were wading in shallow water on the edge of the lake when the alligator attacked.
The parents alerted the nearby lifeguard before some 50 members of the Reedy Creek Fire Rescue, Orange County and the Florida Fish and Wildlife officials joined forces in the search for the missing boy. 
The search for the child will continue until resolved, police officials said.
A Walt Disney World spokesperson attended the news conference on Wednesday morning, saying the "everyone at Disney is devastated" by the incident.