The male tiger, named Rama, died of heart failure at the zoo in the city of Surabaya, on the main island of Java, spokeswoman Veronika Lanu told AFP.
It has been dubbed the “death zoo” as so many animals have died there prematurely because of neglect — including several orangutans, a tiger and a giraffe.
Lanu defended the zoo after Rama’s death, insisting proper procedures had been followed.
“The death was due to natural causes, we provided the best care we could,” she said.
Rama, who was born in the zoo and lived there all his life, died on April 10.
The 16-year-old animal had serious problems with its teeth, had a bad cough and appeared lethargic in the weeks before his death.
Campaigners have criticised the zoo — built a century ago during Dutch colonial rule — for keeping animals in overcrowded cages and enclosures, which are often filthy and in a state of disrepair.
Following his death, it now has only three male Sumatran tigers and six females left.
The management of Surabaya zoo, Indonesia’s largest, has been taken over by the city administration, but the deaths have not stopped and animal welfare groups continue to call for its closure.
The International Union for Conservation of Nature classifies the Sumatran tiger as an endangered species.
There are fewer than 400 remaining in the wild, all on Indonesia’s main western island of Sumatra, according to environmental group WWF.
The creatures are under threat due to destruction of their rainforest habitat to make way for palm oil plantations and poaching.