The Annual HIV Surveillance report from the University of New South Wales' Kirby Institute found 1,235 new cases of the virus were diagnosed in 2013. There were 1,253 new infections in 2012.
"These are the highest levels we've had in 20 years," the institute's associate professor David Wilson said.
While the rates for the past two years have been stable, the 2013 figure represents a 70% rise since 1999, when diagnoses were at their lowest.
Mr Wilson said the evidence suggested that the rise in cases was not due to more testing, but more likely a rise in unprotected sex, particularly among gay men.
The report estimated the number of people living with HIV in Australia at 26,800, but said that about one in seven of these do not know they carry the virus which causes Aids.
Mr Wilson said people were being diagnosed too late in the process, with about 30 % detected well after they should have begun treatment to restore their damaged immune system.
"In some cases, people are living for several years without knowing they are HIV-positive," he said.
"This is a double concern: for their own health and that they could be passing the virus on to others.
"If people wait a long time before getting diagnosed, or if they do not start treatment once diagnosed, it is not as easy to recover."
The good news was that people with HIV were living longer, and the treatment rates for patients in Australia were among the world's best.
In Australia, about 60% of people living with HIV were on treatment in 2013 which suppressed the virus and reduced the risk of transmission.
"This is higher than almost anywhere else in the world and a great achievement," said Mr Wilson. "In comparison, around 25% of people with HIV in the United States are on suppressive therapy."
The release of the data comes ahead of the 20th International Aids Conference in Melbourne next week.