"He is under the control and the protection of the FBI. For us it's not a good thing: it means he is working under the control of American secret services," Putin said in his annual press conference.
"What are they doing to him? What substances are they giving him to say everything they need him to say," Putin added.
Rodchenkov is the former director of the Moscow anti- doping lab. He fled to the United States in 2016 saying he feared for his life after the sudden death of two senior officials in the Russian Anti-Doping Agency (RUSADA). He then provided information which led to an investigation of doping at the Sochi Winter Games in 2014.
Rodchenkov is in the FBI's witness protection programme and has made further revelations about doping.
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Putin accused Rodchenkov of having psychological problems and having been involved in doping.
"How is it that this individual came to head our anti- doping agency?" Putin asked. "This is the mistake of those who made the decision, and I know very well who made the decision."
Putin promised that Russia "will cooperate" with the World Anti-Doping Agency (WADA) and the International Olympic Committee (IOC) "to correct the problems that we have". But he added that Russia would "defend the interests of our athletes, including in civil courts."
The 25 Russian athletes suspended by the IOC for doping in Sochi have announced their intention to go to the Court of Arbitration for Sport. If they lose, they could appeal to a Swiss federal tribunal and finally the European Court of Human Rights.
Russia has always vehemently rejected accusations of state-sponsored doping while accepting that some of its athletes did take banned drugs.
"It's obvious that the scandal is being blown up in the run-up to Russia's domestic political calendar," said Putin, who has announced his intention to seek a fourth term in March.
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