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".