The boy was on holiday with his family, who have not been named.
According to Jerry Demings, Orange County Sheriff, the family were relaxing in a beach area at the edge of the lake when the alligator appeared.
“There is a sandy beach area and the family was out simply relaxing ... and in the water along the lake’s edge at the time the alligator attacked the child.
“It’s my understanding the father was there nearby and the child was playing in the water, just a foot or so into the water, and the alligator came up,” he said.
The boy’s mother also tried to pull her son to safety, according to the Sydney Morning Herald.
More than 50 police officers have spent the past few hours scouring the Seven Seas Lagoon at Disney’s Grand Floridian Resort & Spa.
“As a father and as a grandfather, we’re hoping for the best in these circumstances,” said Sheriff Demings.