The Australian Crime Commission (ACC) said scientists, coaches and support staff were involved in the provision of drugs across multiple sporting codes, without naming any individuals.
In some cases, the drugs were supplied by organised crime syndicates, it said.
Home Affairs Minister Jason Clare said the findings were "shocking and will disgust Australian sports fans".
The president of the World Anti-Doping Agency, John Fahey, described them as "alarming" but not a surprise.
Announcing the findings at a news conference in Canberra, Mr Clare said that "multiple athletes from a number of clubs in major Australian sporting codes are suspected of currently using or having previously used peptides, potentially constituting anti-doping rule violations".
"It's cheating but it's worse than that, it's cheating with the help of criminals," he said.
The commission said it looked at the use of a new form of PIEDs (performance and image enhancing drugs) known as peptides and hormones, which provide effects similar to anabolic steroids."Despite being prohibited substances in professional sport, peptides and hormones are being used by professional athletes in Australia, facilitated by sports scientists, high-performance coaches and sports staff," it said.
"Widespread use of these substances has been identified, or is suspected by the ACC, in a number of professional sporting codes in Australia."
The use of illicit drugs in some sports was thought to be "significantly higher" than official statistics showed, it added.
In some cases, players had been administered with drugs not yet approved for human use, the report also said.
The commission found that organised crime syndicates were involved in the distribution of the banned substances - something Mr Clare, the home affairs minister, called particularly serious.
"Links between organised crime and players exposes players to the risk of being co-opted for match-fixing and this investigation has identified one possible example of that and that is currently under investigation," he said.
Because criminal investigations are under way the report does not go into details, our correspondent says.
The Aussie rules Australian Football League (AFL) and the
National Rugby League (NRL) have said they are already working with the
commission.