The municipality of Tunis posted gory pictures on Facebook of the dead animal’s head next to what appeared to be a bloodied paving slab and another large rock.
“A group of visitors to the zoo threw stones at the head of a crocodile, causing internal haemorrhage that killed it,” it said.
The municipality said the act at the Belvedere Zoo in central Tunis was “savage behaviour”.
The animal died after being hit on the head by two large rocks late Tuesday afternoon, Amor Ennaifer, a vet at the zoo, told AFP.
“It’s terrible. You cannot imagine what animals endure from some visitors,” he said.
“Citizens leave waste and plastic bags… They throw stones at lions and hippos.”
Ennaifer said the zoo has signs and guards but this was not enough, especially during school holidays.
“There are more than 150 species in the zoo. We can’t put a guard in front of each cage,” he said. “People need to be aware of the need to respect animals.”
The behaviour of zoo visitors often causes controversy.
Last year, images showing the zoo covered with litter caused an outcry on social media.
The management blamed zoo visitors for the “catastrophic situation”.