"Of course it came all the way from the top, from the president," Rodchenkov told German public broadcaster ARD in a phone interview, according to a report on the station's website.
"Because only the president can deploy the domestic secret service FSB for such a special task," he is quoted as saying in the German-language report.
Putin "could not deny" knowledge of the scheme, Rodchenkov adds in the report.
Rodchenkov is the former director of the Moscow anti- doping laboratory who fled to the United States in 2016 saying he feared for his life after the sudden death of two senior officials from Russia's anti-doping agency.
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Rodchenkov also said he was convinced that Putin was kept informed about all details of the programme by Vitali Mutko, the then sports minister and current vice premier.
He said that in his own former post, he reported to then-vice sports minister Yuri Nagornikh, who in turn reported to Mutko, who reported to Putin.
Rodchenkov also claimed that, before the 2014 Sochi Games, Russia had run a state-organised doping system at the 2008 Beijing and 2012 London Games.
"I enjoy every day I'm still alive," Rodchenkov said in the interview.
Russia was suspended in August 2016 following revelations of widespread state-sponsored doping uncovered in a report by Richard McLaren on behalf of the World Anti-Doping Agency (WADA).
Neither WADA nor the International Olympic Committee have linked Putin to the conspiracy, only pointing to the sports ministry and slapping lifetime Olympic bans on Nagornikh and Mutko.
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