The female primate named Nanik was suffering from an intestinal tumour and liver problems, Agus Supangkat, spokesman for the zoo in the central city of Surabaya, told AFP.
The 12-year-old ape, who had lost weight and appeared lethargic in recent weeks, died on Saturday, said Supangkat.
She had been living since 2006 at the zoo, which also houses six other female orangutans and three males.
Surabaya Zoo has been dubbed the "death zoo" because so many animals have died there in recent years due to neglect.
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"We have made efforts to improve the welfare of animals at the zoo, including better food and water," he said.
Last year a 30-year-old male giraffe died at the zoo. It was found to have 20 kilograms of plastic in its stomach and to have been suffering from tuberculosis.
Zoo officials believe the plastic came from food wrappers the animal ate after visitors tossed them into its pen over several years.
There are estimated to be 45,000-69,000 Borneo orangutans left in the wild. They are native to the vast island of Borneo, which is shared among Indonesia, Malaysia and Brunei.