Fahey says revelations of alleged widespread performance-enhancing drug use and organised crime links in Australian professional sport are alarming, but not surprising.
"It seems to be history in sport that you'll address these issues only when something surfaces and you'll try to avoid it until that time.
"That was the case in the Olympic movement with doping.
"It's the case in cycling, we've seen so much of in recent times.
"Now sadly it's the case it seems here in Australia.
But he said there would be even darker days to come if sporting bodies did not respond strongly enough to Thursday's revelations.
He said they needed to be asking how the situation had been allowed to reach this point.
"The organisations themselves have to ask a lot of these questions of themselves," he said.
"If you've got a culture within any organisation that believes it may have a problem but does nothing about it or doesn't wish to unearth it you can cover it up."
Fahey said the Australian Sports Anti-Doping Agency (ASADA) was a very good agency and Australia had some very decent sports administrators but it was now clear that doping here was as bad as anywhere else.
He said some banned substances could not be traced in urine and most were unable to be detected more than a week after being ingested, regardless of the testing method used.
He said non-analytical methods, such as the investigation which uncovered Lance Armstrong's systematic performance-enhancing drug use, was a "far more intelligent approach to catching people".
Fahey called on athletes who knew of or were involved in doping to come forward.
Under the WADA code they can earn a 75 per cent penalty reduction for assisting an inquiry, an incentive that helped authorities gather the evidence to bring down Armstrong.