Russia's central election commission last month barred Navalny from taking part in a March presidential election, ruling he was ineligible due to a suspended prison sentence on charges he says were trumped up.
The United States and the European Union criticised the decision, while Navalny said he would encourage people to boycott the vote and would organise a protest rally.
Putin, who is running for a fourth presidential term which polls show he should comfortably win, described US criticism of the central election's commission's decision as crude interference in Russia's internal affairs.
"The person you mentioned (Navalny) is not the only one who hasn't been allowed to run (in the election), but for some reason they are not talking about the other people," Putin told Russian newspaper editors in a meeting broadcast on state TV.
"That obviously shows the US administration's preferences when it comes to who they want to lead other countries, who they want to move forward in Russian politics, and who they'd like to see in the country's leadership."