Putin's intervention came as former Soviet leader Mikhail Gorbachev wrote to International Olympic Committee President Thomas Bach to oppose a blanket ban on the Russian team, saying that a collective sanction was "unacceptable."
Putin did not directly address allegations that Russian government officials helped to cover up hundreds of doping cases, but said the state was resolutely opposed to performance-enhancing drug use.
"In sport there is not and cannot be a place for any doping," Putin said. "Sport must be clean, and an athlete's health must be properly protected."
Putin told a meeting of Russia's cabinet that the commission, under the direction of the Russian Olympic Committee, would provide "rapid development and tough control for the effective realization of a national plan on the fight against doping."
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He added that the commission would be "independent" and would include Russians and foreigners in the fields of medicine, law and sports administration. He did not give a timescale for the commission to begin its work.
"Such a commission should be headed by a person with an absolutely unimpeachable reputation, who has the trust and respect of the Olympic family," Putin said. "There is such a person in our country and he is Vitaly Georgievich Smirnov."
Smirnov once served as the Soviet Union's deputy sports minister and helped to organize the 1980 Olympics in Moscow. Smirnov, a former IOC vice president, was among five IOC members given a "serious warning" in 1999 for their role in the Salt Lake City bid scandal.