"Upon embarking on its investigation the IP (independent person) quickly found a wider means of concealing positive doping results than had been publicly described for Sochi", according to McLaren.
He says labs in Moscow and Sochi protected Russian athletes.
The WADA commission was created to investigate claims by former head of the Moscow anti-doping lab Grigory Rodchenkov, who claimed that a group of Russian sportsmen, including at least 15 medalists, had used performance-enhancing drugs in Sochi with the help of Russian security services and the Sports Ministry.
The report said athletes pre-selected to take part in a doping program had their samples passed through a hole in a lab wall to agents, who found a way to open the tamper-proof bottles, pour in clean urine taken previously from the same athletes, and pass them back into the lab.
The report also implicates illegal doping practices at the 2013 World Athletics Championships in Moscow, and the 2013 World University Games staged in Kazan, where Russian Federation won an unprecedented 292 medals overall.
WADA has called for Russian athletes to be banned from competing in global competitions including Rio, the organization's spokesman Ben Nichols stated in a Tweet.
Several national anti-doping organizations, including from Canada and the USA, were awaiting McLaren's findings to see if they would push for a total ban of the Russian team.
The McLaren probe "reveals most deliberate and disturbing abuse of power ever seen in sport", WADA said through a Nichols tweet, calling the scheme "totally unacceptable".
"The findings of the McLaren report mark a very dark day for sport".
McLaren says he's "supremely confident" in the report's findings.
The report dubbed Russia's program the "disappearing positive methodology".
McLaren said he did not try to speak with Mutko for this report.
The International Olympic Committee immediately scheduled a Tuesday teleconference for its executive board to discuss the matter. The track and field team was subsequently banned from competing in Rio in June.
Russian deputy PM and Olympic committee head Dmitry Kozak has written to Olympic Committee head Thomas Bach and Wada to complain that Wada is trying to "create an global coalition of athletes and organisations supporting a ban on Russian athletes at the Olympic games".
The World Anti-Doping Agency has recommended that Russia's entire team is banned from this summer's Olympic Games.
In Sochi itself, where worldwide observers were scrutinizing 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.
An independent report commissioned by WADA confirmed extraordinary systematic abuse of the anti-doping process across many sports by Russian authorities before and during the Winter Olympics in the Russian city of Sochi in 2014.