Armstrong finally confessed in a television interview last month that he had doped in each of the Tour victories after the U.S. Anti-Doping Agency (USADA) produced evidence it said proved he was a drugs cheat.
"While the ramifications of USADA's impressively thorough investigation into Mr. Armstrong are still being played out, we must not let ourselves forget the fact that this is an individual who masterminded one of the most systematic and widespread doping frauds in the history of sport," Fahey told a WADA media symposium at a London hotel.
"It is not an excuse to say that other riders were doping and therefore I also had to cheat. It is not an excuse to say that the rigorous demands of the sport make it necessary to take performance-enhancing substances.
"It is not an excuse to say that riders in the Tour de France have been seeking an edge ever since the race was founded 100 years ago.
"The reality is that Mr. Armstrong cheated for more than a decade, bullied others into cheating, bullied those who would dare to expose his cheating, and to this day continues to manipulate the facts for his own benefit."
Fahey told a question-and-answer session that the International Cycling Union (UCI) had again called for a truth and reconciliation commission to examine its troubled sport after a series of embarrassing drugs scandals.
The UCI's credibility took a further blow when it disbanded a three-person independent commission set up to investigate whether or not the world governing body had helped Armstrong to conceal his drug-taking without sending it a single document.
It said instead it wanted to be part of a truth and reconciliation commission.
Fahey said he had received a letter late on Monday from the UCI again requesting a truth and reconciliation commission .
He said the UCI had nominated four people from the organisation, not including president Pat McQuaid, who would take part in discussions.
Fahey said WADA had said all along it was more than happy to work out a way to deal "with this constant crisis which seems to surface in cycling".
He said, though, the process had to be under the management and control of the original independent commission.
"So I put those terms back, that's the starting point, it hasn't changed for several weeks. If they are serious they will talk to us," he said.
"Only cycling can heal the problems cycling has, they're independent, they run their own sport, the same as any other sport in the world.
"If the members are prepared to continue to allow this lurching from one crisis to another then I guess we are going to continue to read about turmoil in that sport for some time yet."
Fahey said the Armstrong case showed the growing effectiveness of evidence other than positive drugs tests. American sprinter Marion Jones, who won three gold medals at the 2000 Sydney Olympics, had previously been sanctioned for doping although she also never failed a test.
"Doping athletes should take note that no longer are sanctions based purely on the evidence of blood or urine," Fahey said. "We need to be ever alert to the increasingly sophisticated science available to athletes today and to the growing influence of the underworld."
Fahey said non-analytical evidence was at the heart of the Australian Crime Commission (ACC) report which found widespread use of banned performance-enhancing drugs among professional and amateur athletes with links to gambling and organised crime.
Earlier on Tuesday the National Rugby League said anti-doping officials had met with six leading Australian clubs as a result of the investigation.
"We await the details from this report to see what will come in terms of possible breaches of the rules, and prosecutions of the laws," Fahey said.
In an interview with Reuters television, WADA director general David Howman said the criminal underworld controlled at least 25 percent of world sport. He also said 99 percent of the raw materials used to manufacture illegal drugs came from China .