Professor Peter Collignon, Canberra Hospital's head of infectious diseases, said the cases -- including one patient who had plastic surgery in Mumbai -- were just the "tip of the iceberg".
"There may well be more because it's difficult to pick up this particular gene unless you've got sophisticated testing," Collignon told AFP.
British scientists sparked an angry response from India when they said "medical tourists" were among 37 people who were found to be carrying bacteria with the New Delhi metallo-lactamase-1 (NDM-1) gene.
The gene was identified last year in bacteria carried by a Swedish patient admitted to hospital in India.
The gene, which is found in a number of different bacteria, produces an enzyme that renders even very strong, last resort antibiotics ineffective in combating the bacteria.
Collignon said he treated one of Australia's three cases in Canberra, while there was one each in the eastern states of New South Wales and Queensland.
"We found this multi-resistant, untreatable bug in their urine, luckily not causing too many problems to that person. But it's a real problem if it spreads to others," he said.
"The germ we had was untreatable -- there were no drugs we had that could treat it," he added.
Collignon said his patient caught the bug in intensive care in an Indian hospital after plastic surgery went wrong. But he said one of the three picked up their bug in the general community, indicating the extent of the problem.
"There are likely to be more because what you're picking up in hospitals is just the tip of the iceberg," he said.
"It probably is killing lots of people but it happens in the developing world and there's no way of measuring it."
Collignon blamed the new bugs on the "abuse" of antibiotics in medicine and also in agriculture, saying some countries used them on billions of chickens, which develop bacteria and are then eaten by humans.
The professor, who sits on World Health Organisation panels on antibiotics, called for a worldwide crackdown on antibiotics use along with a major hygiene campaign to stop the bugs spreading.
"All of these systems are interlinked through our food. Wherever we use antibiotics and wherever we over-use them we will get superbugs develop and we will get problems," Collignon said.