The boy was mauled when he went to go to the bathroom behind a bush Saturday on Komodo island, Heru Rudiharto said.
"The Komodo bit him on his waist and tossed him viciously from side to side," Rudiharto said.
"A fishermen, who just happened to be the boy's uncle, threw rocks at the lizard until it let the boy go and fled," he said. "The boy died from massive bleeding half an hour later."
Komodos, the world's largest lizards, are only found in the wild in a small archipelago in eastern Indonesia. Fewer than 4,000 survive.
Rudiharto said the lizards had been living side-by-side with the 1,200 people on Komodo with no fatal incident for 33 years.
"Perhaps the lizards' natural prey has decreased because we are entering the dry season and there has been too much deer hunting," he said.
Komodos can grow to a length of 10 feet and weigh up to 365 pounds.
Thousands of tourists visit Komodo each year to see the lizards in their natural habitat. They are normally shown around the arid and rocky island by guides who carry large, forked sticks to ward of the lizards.