The 3-year-old komodo was found dead at the country's largest zoo in Surabaya, the capital of East Java province, in its enclosure Monday morning, said park spokesman Agus Supangkat.
The cause of the death was not clear, he said.
Scores of animals, including rare and protected ones, have died at the zoo since 2010.
Experts have blamed the deaths on management negligence, cramped enclosures and poor water quality.
According to the Surabaya government, the zoo is home to more than2,800 animals of more than 350 species, the most complete collection in South-East Asia.
DPA