The 18-month-old lion named Michael was found early Tuesday at the zoo in Surabaya, in the east of the main island of Java, said zoo spokesman Agus Supangkat.
"The lion was found hanging from the roof of his cage. He was very young and got his head stuck in cables that keepers use to open and close the cage," Supangkat told AFP.
Supangkat insisted that the death was an accident and not due to negligence. Police were investigating its death, he added.
Among them have been endangered orangutans, a tiger whose food was laced with formaldehyde and a giraffe found dead with a beachball-sized lump of plastic in its stomach, after eating food wrappers thrown into its pen over the years.
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The wildebeest died on Sunday evening of intestinal complications.
Supangkat insisted the wildebeest had been properly fed and said it became sick after days of intense rain and humidity.
African lions are found in most countries in sub-Saharan Africa. The International Union for Conservation of Nature classifies them as vulnerable.