An Australian Crime Commission report in February said dozens of players in the Australian Football League and NRL might have used illegal supplements.
Fahey said doping authorities cannot rely on that background for any potential action against the athletes.
But as motivation for the Australian Sports Anti-Doping Agency, he pointed to the success of the U.S. Anti-Doping Agency's lengthy investigations, which led to Lance Armstrong's eventual confession that he had doped while winning the Tour de France.
"ASADA can't use ACC evidence," Fahey said in an email to The Associated Press on Tuesday. "They must collect their own ... (the) Armstrong investigation took two and a half years, so there is a way to go and NRL stonewalling will further delay resolution."
The reference to "stonewalling" by Fahey, who left Australia on Tuesday to attend a WADA executive board meeting in Montreal, Canada on the weekend, follows a decision last week by lawyers from ASADA and NRL club Cronulla to call off interviews barely before they started.
Cronulla Sharks forward Wade Graham was the first player interviewed by ASADA as it investigates possible use of banned drugs by the NRL club in 2011. But rather than provide any indication of how the testimony would be given, the two sides realized they were far apart on key issues, and ASADA called an early end to the interview.
Under their NRL contracts, players are obliged to give ASADA "reasonable assistance," and that appears to be the main point of difference between Sharks players and ASADA, along with fears that answers could be self-incriminating.
Fahey continued his attack on rugby league administrators in a Sky News interview, saying the AFL, the Melbourne-based organizers for Australian rules football, had been more proactive.
Fahey, who played rugby league and has been involved as an administrator in the sport, said there's been "a profound silence" from the rugby league.
Australia's sports minister Kate Lundy this week said she was concerned about not being able to provide names and details from the crime commission report.
Lundy was a key figure at the Canberra news conference on Feb. 7 that outlined widespread use of prohibited substances including peptides, hormones and illicit drugs, and the infiltration of organized criminal groups in the distribution of performance-enhancing drugs.
"At the time, I felt frustrated because I knew that it would take some time before authorities would be in a position to finalize their investigations and their progress would depend on a lot of co-operation from all parties involved," Lundy said.
Fahey said there was the possibility of reductions in penalties for athletes who provide substantial assistance and testimony in doping investigations.