Zoos Victoria, which runs Melbourne Zoo, Healesville Sanctuary and Werribee Open Range Zoo, has sent an email to its 300,000 members advising them of the new measures.
The message says all giraffe, kangaroo and elephant animal encounters will be closed to the public.
An area of Melbourne Zoo has also been blocked off.
“The public pathway along Trail of the Elephants at Melbourne Zoo, where the critically endangered Asian elephants walk between paddocks, is now blocked to ensure the elephants are not walking over soil that could potentially been brought in from outside the zoo grounds,” the email says.
It also requests certain people avoid visiting zoos at the moment because of FMD.
“If you like with any livestock, except for horses, we ask you to please not visit the zoo at the moment.
“We request that any zoo members or visitors who have recently been to Indonesia to please wait at least 48 hours since returning to Australia before visiting the zoo.”
Zoos Victoria chief executive Dr Jenny Gray said the measures had been brought in to protect the animals out of “an abundance of caution”.
“Over the past week, Zoos Victoria’s veterinarians have liaised with biosecurity officers from state and federal governments, and the Zoo and Aquarium Association, to consider the animal health risks associated with the current outbreak of foot and mouth disease in Indonesia,” she said.
“We are reviewing the situation and our containment measures on a daily basis.”