Now the World Society for the Protection of Animals (WSPA) has written a disturbing report after visiting 10 zoos, which are big tourist attractions in the country.
Chained and dirty
Half the animals were starving and didn't have enough water. And many were forced to entertain visitors too.
Several animals had died from eating sweets and ice-cream thrown by the public. Some had even been given cigarettes.
One orang-utan and baby were living in a filthy cage no bigger than a telephone box.
Animals were chained to their cages and couldn't move properly.
In one zoo in Bali, seven lions were found with sores full of maggots, in cramped cages with no shelter from rain.
At another zoo, three elephants had their legs chained so they couldn't move.
Now WPSA, working with an Indonesian animal charity, want zoos to be licensed and controlled more strictly to stop the cruelty.