Alarmingly, a high rate of chlamydia has been found in girls aged as young as 12.
Professor David Wilson from the Kirby Institute says the figures are the top of the iceberg.
"We know that there are many more Australians out there who are undiagnosed," he said.
"We know that because we've gone out and tested people in rural, remote and urban settings in every state and territory, and we've found one in 20 young Australians have chlamydia.
"We estimate about 500,000 young Australians have chlamydia right now."
Doctors say if chlamydia in any young person is not detected, then there is a significant risk of infertility and complications down the track.
"To start with it's often asymptomatic. They're not aware of it," Professor Wilson said.