But in his report, arbitrator Richard McLaren did not make any recommendations for the future of the Russian team at the Rio Olympics.
In Sochi itself, where worldwide observers were scrutinising the drug tests, positive results could not simply be brushed away, so a system of sample-swapping was put in place with the help of the FSB intelligence service, the report said.
The investigator said allegations made by Grigory Rodchenkov, Moscow's former anti-doping lab director, about sample switching at the Sochi Olympics went much as described in a New York Times story published in May.
"The IOC and IPC must show their commitment to the integrity of sport by banning the whole Russian team from competing next month at the Rio Olympics and Paralympics". "Given the strong stance articulated in Agenda 2020 to protect clean athletes and their track record to date, we would expect the International Olympic Committee to take the strongest possible steps available to them".
The WADA response is a further signal Russian Federation could be facing Olympic expulsion when the 15-member IOC executive board discusses the crisis tonight (NZT). It included the 2013 track world championships in Moscow and was in place during the 2015 swimming world championships in Kazan.
The rest of the plan involved smuggling Russian samples out of the Sochi laboratory through a hole in the wall, an FSB agent taking the caps of the bottles off and Rodchenkov refilling them with urine supplied by the athletes when they knew they were clean.
- The Moscow Laboratory personnel did not have a choice in whether to be involved in the state-directed system.
The Olympics are 18 days away, and the IOC and worldwide sports federations will have to decide the fate of Russia's Olympic team.
The statement said the International Olympic Committee executive board would hold a conference call to discuss immediate sanctions surrounding the Rio Olympics.
The report says 11 positive tests by Russian soccer players were made to disappear in the state-sponsored doping program. Meanwhile, he described tactics he labeled "disappearing positive methodology" that began in 2011, shortly after Russia's disappointing performance at the Vancouver Olympics.
In short, Russia's deputy minister of sports, who was also part of Russia's Olympic Committee, would direct workers at Moscow's anti-doping laboratory of which positive samples to send through and which to hold back.
Mr McLaren said out of 577 positive sample screenings, 312 positive results were held back - or labelled "Save" by the lab workers - but that was only a "small slice" of the data that could have been examined. More than 250 of the 312 "Saves" came from track and field and weightlifting, but other sports involved included swimming, rowing, snowboarding - even table tennis.
Tampered-with bottles could only be detected with microscopic examination, but McLaren said the same type of bottle could safely be used at the 2016 Games now that doping officials are aware of the tactic.
Travis Tygart, the CEO of USADA, called the report proof of a "mind-blowing level of corruption" and urged the worldwide community to come together to ensure that what he called an unprecedented level of criminality never threatens sports again.
While rare for the United States government to take on sports doping cases - it dropped a two-year investigation into famed cyclist Lance Armstrong before it was concluded - the US inquiry will investigate all Russians who may have facilitated doping in the USA, or used USA banks to conduct a doping program.
WADA does not normally make recommendations for discipline when its rules are broken, but prefers to present evidence to the International Olympic Committee and sports federations for them to decide what should be done.
Among those not in favor of a full Russian ban was the head of gymnastics - a sport that was not among the 28 with non-reported positives. The ban was upheld by the IAAF in a vote last month.
But he did say the officials directly named in the report would be provisionally suspended pending a Russian investigation into the report's findings.
McLaren said he was "unwaveringly confident" in his report, and insisted there was no leak, as several sports leaders suggested over the weekend, when draft letters calling for Russia's ban were leaked to the media.