Queensland and Canberra were informed by governing body, the National Rugby League, that they were named in the report, the teams said on their websites on Tuesday.
The report, the result of a year-long probe by Australia's top criminal intelligence unit, has also implicated two Australian Rules football teams.
The revelations have plunged both rival football codes into crisis ahead of the start of their seasons in March and caused shockwaves in Australia, long proud of its image as a nation that plays fair.
NRL chief executive David Smith declined to provide details of the probe into the clubs but said the governing body had been working with the Australian Sports Anti-Doping Authority for a "number of weeks".
"I was given a confidential briefing by the ACC several weeks ago," he told reporters, referring to the Australian Crime Commission, the country's top criminal intelligence unit behind the report released last week.
"And that's what it was. Confidential.
"I can't comment on the outcome on the information we have so far. What I can say is that they're serious matters.
"I have said right from the outset that it involved multiple clubs and multiple players and as a sport we have taken this very seriously in the way we have approached this.
"We will continue to co-operate but we need to make sure that the process is fair."
The clubs were not given any details about the probe, but said in their statements they would co-operate fully with the NRL and ASADA.
Smith said the clubs would be briefed by ASADA on Tuesday and called on people to come forward.
"History has shown it's always better to step forward and I would encourage anybody to do that," he said. "I'm not pre-judging anybody. I think that's the best way to go."
The Australian Crime Commission report released last week said it had found "widespread" use of banned performance- enhancing drugs among professional and amateur athletes, with links to gambling and organized crime.
The report has fuelled anger among Australia's top athletes and politicians, who have criticized the report's authors for being short on details and for blackening the name of clean sportspeople.
Newcastle coach Wayne Bennett said auditors had gone through his club's records dating back to 2005.
"They want us to confess to something. I'm racking my head what we've got to confess to," Bennett, one of the league's most successful coaches, told reporters.
"I've been through the staff, I've checked with all the players ... Whatever they're looking for, it hasn't happened in the past 18 months. So after that I've got no idea."
Penrith captain Kevin Kingston said he was confident his club was clean.
"We trust our sports scientists. We don't take anything out of the ordinary. I barely take protein myself," he told reporters at Sydney airport.
"I don't think there is a drug problem at our club."
One Australian Rules football team, the Essendon Bombers, have confirmed they are under scrutiny by ASADA for their use of supplements given to players.
The governing body Australian Football League has declined to name the second club being probed but has confirmed one player is under suspicion.