"There isn't and cannot be any support on the government level of violations in sport, especially on the question of doping," Putin said at the annual economic forum in Saint Petersburg.
The IAAF is voting on Friday on whether to lift Russia's provisional suspension, imposed in November over a bombshell report containing evidence of state-sponsored doping and corruption in Russian athletics.
Moscow is furiously campaigning to overturn the ban, which could see Russian track and field stars sidelined from the Rio Games in August.
"There cannot be collective responsibility of all athletes," Putin said. "The whole team cannot bear responsibility for one who committed a violation" of anti-doping regulations.
Since the suspension, Russian authorities have vowed to revamp the country's scandal-ridden anti-doping system, announcing a series of measures to fulfil IAAF and World Anti-Doping Agency (WADA) requirements.
These measures include the introduction of compulsory anti-doping classes in schools across the country and additional doping tests for athletes hoping to compete in Rio.
Putin also warned against attempts to politicise the doping scandal and form an "anti-Russian position".
"And if someone tries to politicise something in this field, I think this is a big mistake.
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