A "systematic and centralized cover-up" benefited more than 1,000 Russian athletes across 30 sports, said Canadian law professor Richard McLaren in an update to a report first published in July.
McLaren alleged an "institutional conspiracy" among officials within the Russian ministry of sport and state security services that resulted in the London 2012 Games being corrupted "on an unprecedented scale."
"We know for sure it went to the Deputy Minister of Sport level -- beyond that we have no evidence to indicate that it went any further," McLaren told CNN.
Hours after the report was published, the International Olympic Committee announced it would retest all 254 samples
collected from Russian athletes who took part in the 2014 Winter Olympics in Sochi.
The Kremlin said it would study the report thoroughly, but will "refrain from forming an emotional response to allegations of the 'state conspiracy,'" according to state news agency Sputnik.
Russia's ministry for sport denied a state-sponsored program to aid doping in sports and stressed it is "continuing its fight against doping from the position of 'zero tolerance.'"
The report found:
- More than 1,000 Russian athletes benefited from doping
- There was an "institutional conspiracy" among athletes and officials within the Ministry of Sport and the FSB
- "Systematic and centralized cover up" in the run up to the London 2012 Summer Olympics which continued until 2015
- London 2012 games corrupted "on an unprecedented scale"
- Swapping of urine samples became a regular practice after the 2014 Sochi Games
- Male DNA found in samples from two female hockey players
McLaren said it was impossible to say how far the conspiracy stretched back. "For years, international sports competitions have unknowingly been hijacked by the Russians. Coaches and athletes have been playing on an uneven field. Sports fans and spectators have been deceived."
The WADA investigation was spurred by claims made by former Russian anti-doping laboratory director Grigory Rodchenkov last year to the New York Times that he was ordered to cover up the drug use of at least 15 Sochi 2014 medal winners.
Rodchenkov alleged that he assisted in doctoring urine samples provided by Russian athletes during overnight shifts at the Sochi Games.
He also accused the Russian secret service of providing active assistance with the cover-up, which he says took place before, during and after the Sochi Olympics.
The second part of the McLaren report said there was "conclusive" forensic evidence that sample bottles had been tampered with and the contents altered.
The technique was refined over the course of the London 2012 Olympics, 2013 World Athletics Championships in Moscow and the 2014 Sochi Winter Olympics where a now "fail safe" system was in place to protect likely Russian medal winners, the report found.
In Sochi, two female ice hockey players' samples were found to contain male DNA, while two gold medalists and one female silver medalist were found to have "physiologically impossible salt readings."
Also, 44 of the samples examined -- including 12 from medal-winning athletes -- had scratches and marks on the caps of the bottles, indicating tampering.
Fifteen Russian medal-winning athletes from London 2012 were also found to have been involved in doping.
Russia won 72 medals at the London Games, 21 of which were gold, and 33 medals at Sochi 2014, 13 of which were gold.
"The Russian Olympic team corrupted the London games on an unprecedented scale - the extent of which will probably never be fully established," the report added.
The scope of the subversion is "alarming," according to WADA president Sir Craig Reedie, while the findings show a "fundamental attack on the integrity of the Olympic Games and on sport in general," said an IOC statement.
Russian MP Dmitry Svishchev said the accusations were "unsubstantiated," while politician Igor Lebedev said "there were no facts and no evidence" and Stanislav Pozdnyakov, of the Russian Olympic Committee, told the TASS new agency it was "strange" the report did not name names.
"There is evidence that's not being published because some of the evidence may not be sufficient enough to support an anti-doping rule violation. Some of it definitely is," McLaren told CNN.
"That's up to other people to decide not me. That's why I didn't publish their names."
The Russian Anti-Doping Agency (RUSADA) is set to meet on Dec. 15 to discuss the report. Its new head, former pole vaulter Yelena Isinbayeva, acknowledged it had a "very big job" to restore confidence in Russia's sporting landscape but added she was "optimistic."
"All the previous people working for RUSADA have now left and we will work hard to prove to the world that Russia can be trusted," Isinbayeva told InsidetheGames.
"I want to rebuild RUSADA in my own clean image."
The International Association of Athletics Federations (IAAF) says it agrees with Professor McLaren that "it is time that this manipulation stops" and says it is pursuing "a more specific, intelligence-based retesting program."
The International Paralympic Committee said the findings of the report were "unprecedented and astonishing."
"They strike right at the heart of the integrity and ethics of sport," the IPC said in a statement.
Professor McLaren said it is not for him to decide whether Russia should compete in the 2018 Winter Olympics in Pyeongchang, but said he was confident Russia could reform. He wouldn't be drawn on the merits of the forthcoming soccer World Cup in Russia in 2018.
In November, Russian president Vladimir Putin signed a new law to criminalize any encouragement for doping, national news agency Tass reported.
Anyone found guilty of inducing an athlete to use drugs faces a fine of up to 1.1 million rubles ($11,400) or a jail term of up to three years, plus suspension from "professional activities" for up to five years, depending on the circumstances.
Following the initial report, WADA called for a blanket ban on Russian competitors at Rio 2016, but the International Olympic Committee ruled each sporting federation should decide whether Russians be admitted.
Russia's track and field team and weightlifting squad were eventually excluded from August's Games.