They found more than 20% of silver gulls nationwide carrying bacteria such as E. coli, which can cause urinary tract and blood infections and sepsis.
The research has raised fears that the antibiotic-resistant bacteria- similar to superbugs which have hit hospitals - could infect humans and other animals.
Scientists have described it as a "wake-up call".
The birds are believed to have contracted the bugs from scavenging in rubbish and sewage.
The scientists who conducted the research on behalf of Murdoch University in Perth have said it is "eye-opening", The Guardian reported.
"I think that it is a wake-up call for all government and various agencies, like water treatment and big councils that manage waste, to properly work collaboratively to tackle this issue," said Dr Sam Abraham, a lecturer in veterinary and medical infectious diseases.
Humans could contract the bacteria if they touched the seagull faeces, but the risk is considered low if they wash their hands afterwards.
The study showed some bugs found in the faeces were resistant to common antibiotic medications such as cephalosporin and fluoroquinolone.
One sample showed resistance to carbapenem, which is a last-resort drug used for severe and high-risk infections.
