"We do not support what the hackers do, but what they did cannot but be of interest to the international community, and most of all to the sports community," Putin said at a regional leaders summit in Central Asian Kyrgyzstan, Russian news agencies reported.
"It raises lots of questions."
WADA said in a statement earlier this week that the Russian cyber-espionage group Tsar Team (APT28), also known as Fancy Bears, had broken into its Anti-Doping Administration and Management System (ADAMS).
Putin slammed the fact that "healthy athletes" had been allowed to take forbidden medication while Russia's Paralympians had been excluded from the Rio Paralympics "under suspicion of having taken some kind of drugs".
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Russia is still smarting after its track and field athletes were banned from the Olympics and its entire Paralympics team turfed out of their Games over evidence of state-sponsored doping.
WADA called the hack "retaliation" after it released reports detailing the cheating and called on Russia to help stop the hacking of its computer systems.