An independent investigation claims the Russian sports ministry "directed, controlled and manipulated" the drug tests taken by athletes between 2011 and 2015.
WADA's findings deepen the doping crisis surrounding Russian athletes, sparking calls to withdraw Russia's invitation to the upcoming Olympics.
The independent "McLaren Report", named after its author Dr Richard McLaren, found Russia's government and intelligence service together operated a state-sponsored doping program.
Running between 2011 and 2015 across the vast majority of summer and winter Olympic sports, the program involved switching athletes' urine samples with drug-free, 'clean' samples.
That covered up almost 600 positive tests across 30 different sports and a wide range of events, including the 2014 Winter Olympics in Sochi, Russia, and the 2012 London Olympics.
Dr McLaren says Russia's Federal Security Service, the FSB, and its Centre for Sports Preparation, the CSP, supported the cover-ups via two anti-doping laboratories during the Sochi games.
"First, the Moscow laboratory operated for the protection of doped Russian athletes within a state-directed, fail-safe system, which we describe in the report as the 'disappearing positive methodology'. Second, the Sochi laboratory operated a unique sample-swapping methodology to enable doped Russian athletes to compete at the winter Olympic games."
The report says it wasn't confined to Sochi and London.
It says Russia's cheating extended to athletics and swimming world championships, and to paralympians.
The system was allegedly set up after what Russian authorities felt was a poor medal count by its 2010 Winter Olympics team in Vancouver, Canada.
Dr McLaren says Russia's sport ministry "directed, controlled and oversaw" the manipulation of test results.
"We do know that every single positive first screened in the Moscow lab was sent up the chain of command and an order sent back down. Now that has to affect every single sport across the board. From all of this comes a picture that emerges of an intertwined network of state involvement through the Ministry of Sport and through this CSP, and with the FSB, in the operations of both Moscow and Sochi labs. It was a fail-safe method of permitting cheating Russian athletes to compete while using performance-enhancing substances."
The findings appear to vindicate the man at the centre of the scandal, whistleblower Grigory Rodchenkov, the former head of Russia's anti-doping agency.
In May he claimed he helped dozens of athletes to cheat, shortly after he fled to the United States.
Russian President Vladimir Putin has condemned doping and denies the allegations, saying they are politically motivated, a comment aimed at Dr Rodchenkov.
Dmitry Babach, an analyst for Russian news network Sputnik International, believes most Russians feel the same way.
"The majority is angry with speedy conclusions. I mean you're already saying that this is an industrial-sized breach of rules, but it is all based on the testimony of one person. The problem is that how reliable is this witness? And the fact that WADA's report quotes him, I quote, 'a truthful and honest man' is shocking, because it is not up to WADA to decide who is honest and who is dishonest."
Russia's track and field athletes are already banned from competing in the Olympics by the International Association of Athletics' Federations over widespread doping in the sport.
But calls are growing for the International Olympic Committee to ban all Russian athletes.
In a statement, the IOC said WADA's findings show a "shocking and unprecedented attack on the integrity of sports and the Olympic Games".
It added it will not "hesitate to take the toughest sanctions available".
Former British track and field Olympian, Jenny Meadows, told the BBC she hopes the IOC rules Russia out of Rio.
"I think we really need to see the International Olympic Committee come out with an announcement very very soon, and I'm obviously hoping that would be a blanket ban on the Russian athletics federation, and every single Russian sport in the Rio Games."
320 Russian athletes should be travelling to Brazil, and Olympic organisers have just days to decide if they'll be allowed to compete.
If they are banned, some say it will have major ramifications.
"Taking part in the Olympics was the goal of all my life. And if they steal my dream now it will be very hard and painful for me."
