The body of the male rhino was found inside West Java's Ujung Kulon national park, the creature's last remaining habitat.
Its death was believed to be from old age rather than poaching.
The animal has been driven to the brink of extinction as their horns are highly valued in traditional Chinese and Korean medicine, although most countries in the region have banned the trade.
The 40-year-old rhino didn't had any offspring, he added.
Javan and Sumatran rhinos are classified as "critically endangered" by the International Union for Conservation of Nature (IUCN).
The Javan rhino is distinguished from African rhinos by its smaller size, single horn and loose skin folds which give it the appearance of wearing armour plating.
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